Starting phenix.real_space_refine on Sun Jul 27 17:58:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xck_33123/07_2025/7xck_33123.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xck_33123/07_2025/7xck_33123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xck_33123/07_2025/7xck_33123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xck_33123/07_2025/7xck_33123.map" model { file = "/net/cci-nas-00/data/ceres_data/7xck_33123/07_2025/7xck_33123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xck_33123/07_2025/7xck_33123.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4868 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 3473 2.51 5 N 927 2.21 5 O 1067 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 5488 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1688 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 210} Chain breaks: 1 Chain: "B" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1615 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200} Chain: "M" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2147 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 16, 'TRANS': 252} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} 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: 6.04, per 1000 atoms: 1.10 Number of scatterers: 5488 At special positions: 0 Unit cell: (113.9, 61.64, 122.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 1067 8.00 N 927 7.00 C 3473 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 210 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS M 336 " - pdb=" SG CYS M 361 " distance=2.03 Simple disulfide: pdb=" SG CYS M 379 " - pdb=" SG CYS M 432 " distance=2.04 Simple disulfide: pdb=" SG CYS M 480 " - pdb=" SG CYS M 488 " distance=2.03 Simple disulfide: pdb=" SG CYS M 538 " - pdb=" SG CYS M 590 " 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 BETA1-4 " NAG C 1 " - " NAG C 2 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG C 1 " - " ASN M 343 " Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 1.3 seconds 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1302 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 14 sheets defined 9.7% alpha, 38.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.646A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.942A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 80 through 84 removed outlier: 4.031A pdb=" N PHE B 84 " --> pdb=" O PRO B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 188 removed outlier: 3.542A pdb=" N LYS B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 338 through 343 Processing helix chain 'M' and resid 365 through 369 Processing helix chain 'M' and resid 383 through 390 removed outlier: 3.529A pdb=" N LEU M 387 " --> pdb=" O PRO M 384 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASN M 388 " --> pdb=" O THR M 385 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU M 390 " --> pdb=" O LEU M 387 " (cutoff:3.500A) Processing helix chain 'M' and resid 403 through 410 removed outlier: 3.521A pdb=" N GLU M 406 " --> pdb=" O ARG M 403 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL M 407 " --> pdb=" O GLY M 404 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG M 408 " --> pdb=" O ASP M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 422 Processing helix chain 'M' and resid 438 through 443 removed outlier: 3.707A pdb=" N SER M 443 " --> pdb=" O ASN M 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.515A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TRP A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASN A 116 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.515A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TRP A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 138 removed outlier: 6.127A pdb=" N TYR A 190 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 134 through 138 removed outlier: 6.127A pdb=" N TYR A 190 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 165 through 168 Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.402A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N TYR B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.402A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 116 through 118 removed outlier: 3.957A pdb=" N VAL B 133 " --> pdb=" O PHE B 118 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN B 138 " --> pdb=" O TYR B 173 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR B 173 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 145 through 149 Processing sheet with id=AB3, first strand: chain 'M' and resid 325 through 328 removed outlier: 5.842A pdb=" N ASP M 574 " --> pdb=" O ILE M 587 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY M 566 " --> pdb=" O ASP M 574 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 354 through 358 Processing sheet with id=AB5, first strand: chain 'M' and resid 452 through 454 209 hydrogen bonds defined for protein. 513 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 948 1.32 - 1.45: 1605 1.45 - 1.58: 3044 1.58 - 1.71: 0 1.71 - 1.84: 24 Bond restraints: 5621 Sorted by residual: bond pdb=" C ALA M 344 " pdb=" N THR M 345 " ideal model delta sigma weight residual 1.335 1.278 0.057 1.25e-02 6.40e+03 2.05e+01 bond pdb=" CA ALA M 344 " pdb=" CB ALA M 344 " ideal model delta sigma weight residual 1.528 1.474 0.054 1.58e-02 4.01e+03 1.15e+01 bond pdb=" C ALA M 344 " pdb=" O ALA M 344 " ideal model delta sigma weight residual 1.235 1.201 0.034 1.20e-02 6.94e+03 8.18e+00 bond pdb=" C ASN M 343 " pdb=" O ASN M 343 " ideal model delta sigma weight residual 1.235 1.197 0.038 1.32e-02 5.74e+03 8.17e+00 bond pdb=" CA ALA M 344 " pdb=" C ALA M 344 " ideal model delta sigma weight residual 1.524 1.486 0.038 1.33e-02 5.65e+03 8.00e+00 ... (remaining 5616 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 7496 2.21 - 4.43: 120 4.43 - 6.64: 25 6.64 - 8.85: 2 8.85 - 11.07: 1 Bond angle restraints: 7644 Sorted by residual: angle pdb=" CA ASN M 334 " pdb=" C ASN M 334 " pdb=" O ASN M 334 " ideal model delta sigma weight residual 121.15 116.26 4.89 1.10e+00 8.26e-01 1.98e+01 angle pdb=" C VAL B 150 " pdb=" N ASP B 151 " pdb=" CA ASP B 151 " ideal model delta sigma weight residual 121.54 129.19 -7.65 1.91e+00 2.74e-01 1.60e+01 angle pdb=" C ASN M 343 " pdb=" CA ASN M 343 " pdb=" CB ASN M 343 " ideal model delta sigma weight residual 111.02 104.60 6.42 1.61e+00 3.86e-01 1.59e+01 angle pdb=" C PRO A 161 " pdb=" N GLU A 162 " pdb=" CA GLU A 162 " ideal model delta sigma weight residual 120.26 125.14 -4.88 1.34e+00 5.57e-01 1.33e+01 angle pdb=" C SER B 95 " pdb=" CA SER B 95 " pdb=" CB SER B 95 " ideal model delta sigma weight residual 115.89 111.20 4.69 1.32e+00 5.74e-01 1.26e+01 ... (remaining 7639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 3108 17.59 - 35.17: 228 35.17 - 52.76: 47 52.76 - 70.34: 5 70.34 - 87.93: 4 Dihedral angle restraints: 3392 sinusoidal: 1356 harmonic: 2036 Sorted by residual: dihedral pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " pdb=" SG CYS A 210 " pdb=" CB CYS A 210 " ideal model delta sinusoidal sigma weight residual 93.00 162.64 -69.64 1 1.00e+01 1.00e-02 6.26e+01 dihedral pdb=" CB CYS M 538 " pdb=" SG CYS M 538 " pdb=" SG CYS M 590 " pdb=" CB CYS M 590 " ideal model delta sinusoidal sigma weight residual -86.00 -38.35 -47.65 1 1.00e+01 1.00e-02 3.13e+01 dihedral pdb=" CB CYS M 379 " pdb=" SG CYS M 379 " pdb=" SG CYS M 432 " pdb=" CB CYS M 432 " ideal model delta sinusoidal sigma weight residual -86.00 -51.56 -34.44 1 1.00e+01 1.00e-02 1.68e+01 ... (remaining 3389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 855 0.142 - 0.284: 2 0.284 - 0.425: 0 0.425 - 0.567: 0 0.567 - 0.709: 1 Chirality restraints: 858 Sorted by residual: chirality pdb=" C1 FUC C 3 " pdb=" O6 NAG C 1 " pdb=" C2 FUC C 3 " pdb=" O5 FUC C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.19e+01 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN M 343 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CA VAL A 37 " pdb=" N VAL A 37 " pdb=" C VAL A 37 " pdb=" CB VAL A 37 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.69e-01 ... (remaining 855 not shown) Planarity restraints: 982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.045 2.00e-02 2.50e+03 3.72e-02 1.73e+01 pdb=" C7 NAG C 1 " 0.011 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.034 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.060 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " 0.041 2.00e-02 2.50e+03 3.36e-02 1.41e+01 pdb=" C7 NAG C 2 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " 0.032 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " -0.052 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA M 520 " 0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO M 521 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO M 521 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO M 521 " 0.036 5.00e-02 4.00e+02 ... (remaining 979 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 246 2.72 - 3.27: 5007 3.27 - 3.81: 8362 3.81 - 4.36: 10652 4.36 - 4.90: 18600 Nonbonded interactions: 42867 Sorted by model distance: nonbonded pdb=" OH TYR M 369 " pdb=" O PRO M 384 " model vdw 2.179 3.040 nonbonded pdb=" OG SER B 64 " pdb=" OG1 THR B 75 " model vdw 2.198 3.040 nonbonded pdb=" OG1 THR A 149 " pdb=" O VAL A 198 " model vdw 2.228 3.040 nonbonded pdb=" OE1 GLU B 105 " pdb=" OH TYR B 173 " model vdw 2.296 3.040 nonbonded pdb=" O ASP M 442 " pdb=" ND2 ASN M 448 " model vdw 2.307 3.120 ... (remaining 42862 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: 15.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.140 Find NCS groups from input model: 0.060 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:13.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 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 : 0.004 0.057 5632 Z= 0.203 Angle : 0.723 11.067 7669 Z= 0.392 Chirality : 0.052 0.709 858 Planarity : 0.006 0.065 981 Dihedral : 12.630 87.930 2066 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.60 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.32), residues: 696 helix: -3.99 (0.85), residues: 20 sheet: 0.21 (0.33), residues: 271 loop : -0.98 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 436 HIS 0.004 0.001 HIS M 519 PHE 0.012 0.001 PHE M 374 TYR 0.007 0.001 TYR A 159 ARG 0.002 0.000 ARG M 346 Details of bonding type rmsd link_NAG-ASN : bond 0.02761 ( 1) link_NAG-ASN : angle 4.16457 ( 3) link_BETA1-4 : bond 0.00179 ( 1) link_BETA1-4 : angle 2.72332 ( 3) hydrogen bonds : bond 0.14772 ( 181) hydrogen bonds : angle 7.19690 ( 513) link_BETA1-6 : bond 0.01807 ( 1) link_BETA1-6 : angle 2.90036 ( 3) SS BOND : bond 0.00609 ( 8) SS BOND : angle 1.26856 ( 16) covalent geometry : bond 0.00357 ( 5621) covalent geometry : angle 0.71268 ( 7644) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.635 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 1.4096 time to fit residues: 101.2736 Evaluate side-chains 57 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 17 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 0.0070 chunk 20 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 GLN M 417 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.183202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.118206 restraints weight = 6043.238| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.51 r_work: 0.3279 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.0785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5632 Z= 0.124 Angle : 0.598 9.055 7669 Z= 0.308 Chirality : 0.046 0.138 858 Planarity : 0.006 0.060 981 Dihedral : 4.968 20.301 823 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.47 % Allowed : 5.92 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.33), residues: 696 helix: -4.40 (0.55), residues: 26 sheet: 0.37 (0.33), residues: 268 loop : -0.94 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 47 HIS 0.004 0.001 HIS B 92 PHE 0.013 0.001 PHE M 377 TYR 0.008 0.001 TYR M 369 ARG 0.004 0.000 ARG B 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00416 ( 1) link_NAG-ASN : angle 2.09752 ( 3) link_BETA1-4 : bond 0.00116 ( 1) link_BETA1-4 : angle 2.32415 ( 3) hydrogen bonds : bond 0.03498 ( 181) hydrogen bonds : angle 5.75943 ( 513) link_BETA1-6 : bond 0.00217 ( 1) link_BETA1-6 : angle 1.91816 ( 3) SS BOND : bond 0.00606 ( 8) SS BOND : angle 1.34283 ( 16) covalent geometry : bond 0.00285 ( 5621) covalent geometry : angle 0.59160 ( 7644) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.616 Fit side-chains REVERT: A 43 GLN cc_start: 0.7919 (mm-40) cc_final: 0.7302 (mp10) REVERT: A 82 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7601 (tp30) REVERT: B 117 ILE cc_start: 0.6515 (tt) cc_final: 0.6080 (mm) REVERT: M 357 ARG cc_start: 0.8697 (ttp-170) cc_final: 0.8263 (ttp80) REVERT: M 405 ASP cc_start: 0.7846 (p0) cc_final: 0.7593 (p0) REVERT: M 586 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7947 (m-30) outliers start: 15 outliers final: 5 residues processed: 70 average time/residue: 1.4251 time to fit residues: 104.4252 Evaluate side-chains 64 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 553 THR Chi-restraints excluded: chain M residue 586 ASP Chi-restraints excluded: chain M residue 588 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 60 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 0.0010 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- 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 = 0.4162 r_free = 0.4162 target = 0.182541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.118930 restraints weight = 6045.923| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.43 r_work: 0.3311 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 5632 Z= 0.257 Angle : 0.703 8.423 7669 Z= 0.366 Chirality : 0.050 0.177 858 Planarity : 0.006 0.064 981 Dihedral : 5.458 20.159 823 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.63 % Allowed : 11.51 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.32), residues: 696 helix: -4.39 (0.49), residues: 26 sheet: 0.10 (0.32), residues: 281 loop : -1.07 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 50 HIS 0.006 0.002 HIS B 92 PHE 0.026 0.002 PHE M 377 TYR 0.016 0.002 TYR B 37 ARG 0.005 0.001 ARG B 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00698 ( 1) link_NAG-ASN : angle 1.61542 ( 3) link_BETA1-4 : bond 0.00054 ( 1) link_BETA1-4 : angle 2.88076 ( 3) hydrogen bonds : bond 0.04427 ( 181) hydrogen bonds : angle 5.80391 ( 513) link_BETA1-6 : bond 0.00423 ( 1) link_BETA1-6 : angle 1.65762 ( 3) SS BOND : bond 0.01187 ( 8) SS BOND : angle 2.15799 ( 16) covalent geometry : bond 0.00627 ( 5621) covalent geometry : angle 0.69338 ( 7644) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.564 Fit side-chains REVERT: A 43 GLN cc_start: 0.8502 (mm-40) cc_final: 0.7955 (mp10) REVERT: B 117 ILE cc_start: 0.6850 (tt) cc_final: 0.6472 (mm) REVERT: M 357 ARG cc_start: 0.8943 (ttp-170) cc_final: 0.8631 (ttp-170) REVERT: M 403 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7212 (ttt-90) REVERT: M 461 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7625 (pp) REVERT: M 574 ASP cc_start: 0.8184 (p0) cc_final: 0.7737 (p0) REVERT: M 586 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8188 (m-30) outliers start: 16 outliers final: 7 residues processed: 71 average time/residue: 1.4327 time to fit residues: 106.4221 Evaluate side-chains 69 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 403 ARG Chi-restraints excluded: chain M residue 461 LEU Chi-restraints excluded: chain M residue 470 THR Chi-restraints excluded: chain M residue 553 THR Chi-restraints excluded: chain M residue 586 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 0.1980 chunk 16 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.4181 r_free = 0.4181 target = 0.184460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.121369 restraints weight = 6187.483| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.45 r_work: 0.3338 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 5632 Z= 0.152 Angle : 0.615 10.772 7669 Z= 0.318 Chirality : 0.046 0.146 858 Planarity : 0.006 0.066 981 Dihedral : 5.068 20.848 823 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.14 % Allowed : 15.13 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.32), residues: 696 helix: -4.30 (0.51), residues: 26 sheet: 0.38 (0.33), residues: 268 loop : -1.10 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 47 HIS 0.005 0.001 HIS B 92 PHE 0.015 0.001 PHE M 377 TYR 0.009 0.001 TYR B 140 ARG 0.004 0.000 ARG B 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00524 ( 1) link_NAG-ASN : angle 1.65991 ( 3) link_BETA1-4 : bond 0.00167 ( 1) link_BETA1-4 : angle 2.41814 ( 3) hydrogen bonds : bond 0.03547 ( 181) hydrogen bonds : angle 5.53412 ( 513) link_BETA1-6 : bond 0.00136 ( 1) link_BETA1-6 : angle 1.52191 ( 3) SS BOND : bond 0.00758 ( 8) SS BOND : angle 1.53593 ( 16) covalent geometry : bond 0.00361 ( 5621) covalent geometry : angle 0.60885 ( 7644) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.555 Fit side-chains REVERT: A 43 GLN cc_start: 0.8424 (mm-40) cc_final: 0.7908 (mp10) REVERT: A 46 GLU cc_start: 0.8755 (tt0) cc_final: 0.8534 (tt0) REVERT: A 89 ASP cc_start: 0.8333 (m-30) cc_final: 0.7476 (t0) REVERT: B 117 ILE cc_start: 0.6787 (tt) cc_final: 0.6414 (mm) REVERT: M 357 ARG cc_start: 0.8943 (ttp-170) cc_final: 0.8567 (ttp-170) REVERT: M 403 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7066 (ttt-90) REVERT: M 461 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7477 (pp) REVERT: M 574 ASP cc_start: 0.8199 (p0) cc_final: 0.7724 (p0) REVERT: M 586 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8080 (m-30) outliers start: 13 outliers final: 8 residues processed: 67 average time/residue: 1.6788 time to fit residues: 117.7803 Evaluate side-chains 67 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 403 ARG Chi-restraints excluded: chain M residue 461 LEU Chi-restraints excluded: chain M residue 553 THR Chi-restraints excluded: chain M residue 572 THR Chi-restraints excluded: chain M residue 586 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 57 optimal weight: 0.0070 chunk 60 optimal weight: 0.0470 chunk 30 optimal weight: 0.3980 chunk 17 optimal weight: 6.9990 chunk 49 optimal weight: 40.0000 overall best weight: 1.2900 ------------------------------------------------------------------------------- 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 = 0.4179 r_free = 0.4179 target = 0.184157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.121101 restraints weight = 6080.202| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.43 r_work: 0.3337 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5632 Z= 0.167 Angle : 0.630 10.157 7669 Z= 0.324 Chirality : 0.046 0.151 858 Planarity : 0.006 0.065 981 Dihedral : 5.050 20.763 823 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.62 % Allowed : 14.14 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.32), residues: 696 helix: -4.28 (0.52), residues: 26 sheet: 0.43 (0.33), residues: 265 loop : -1.12 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 47 HIS 0.005 0.001 HIS B 92 PHE 0.018 0.002 PHE M 377 TYR 0.010 0.001 TYR B 37 ARG 0.004 0.000 ARG B 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00553 ( 1) link_NAG-ASN : angle 1.52425 ( 3) link_BETA1-4 : bond 0.00193 ( 1) link_BETA1-4 : angle 2.43678 ( 3) hydrogen bonds : bond 0.03625 ( 181) hydrogen bonds : angle 5.55167 ( 513) link_BETA1-6 : bond 0.00144 ( 1) link_BETA1-6 : angle 1.54874 ( 3) SS BOND : bond 0.00837 ( 8) SS BOND : angle 1.48255 ( 16) covalent geometry : bond 0.00402 ( 5621) covalent geometry : angle 0.62354 ( 7644) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.634 Fit side-chains REVERT: A 43 GLN cc_start: 0.8496 (mm-40) cc_final: 0.7952 (mp10) REVERT: A 46 GLU cc_start: 0.8772 (tt0) cc_final: 0.8564 (tt0) REVERT: A 89 ASP cc_start: 0.8313 (m-30) cc_final: 0.7487 (t0) REVERT: B 117 ILE cc_start: 0.6768 (tt) cc_final: 0.6409 (mm) REVERT: B 166 GLN cc_start: 0.7174 (tt0) cc_final: 0.6779 (tt0) REVERT: M 357 ARG cc_start: 0.8953 (ttp-170) cc_final: 0.8460 (ttp80) REVERT: M 403 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7192 (ttt-90) REVERT: M 461 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7521 (pp) REVERT: M 465 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8078 (tt0) REVERT: M 574 ASP cc_start: 0.8142 (p0) cc_final: 0.7648 (p0) REVERT: M 586 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.8091 (m-30) outliers start: 22 outliers final: 11 residues processed: 73 average time/residue: 1.3481 time to fit residues: 102.9822 Evaluate side-chains 73 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 403 ARG Chi-restraints excluded: chain M residue 461 LEU Chi-restraints excluded: chain M residue 465 GLU Chi-restraints excluded: chain M residue 553 THR Chi-restraints excluded: chain M residue 572 THR Chi-restraints excluded: chain M residue 581 THR Chi-restraints excluded: chain M residue 586 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 505 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.183935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.120565 restraints weight = 6097.983| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.43 r_work: 0.3335 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5632 Z= 0.178 Angle : 0.659 9.805 7669 Z= 0.338 Chirality : 0.048 0.275 858 Planarity : 0.006 0.067 981 Dihedral : 5.078 20.657 823 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.45 % Allowed : 15.46 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.32), residues: 696 helix: -4.24 (0.54), residues: 26 sheet: 0.56 (0.33), residues: 262 loop : -1.12 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 50 HIS 0.005 0.001 HIS B 92 PHE 0.019 0.002 PHE M 377 TYR 0.012 0.001 TYR M 380 ARG 0.006 0.000 ARG B 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 1) link_NAG-ASN : angle 1.46472 ( 3) link_BETA1-4 : bond 0.00181 ( 1) link_BETA1-4 : angle 2.43545 ( 3) hydrogen bonds : bond 0.03764 ( 181) hydrogen bonds : angle 5.49166 ( 513) link_BETA1-6 : bond 0.00172 ( 1) link_BETA1-6 : angle 1.54976 ( 3) SS BOND : bond 0.01158 ( 8) SS BOND : angle 1.88539 ( 16) covalent geometry : bond 0.00428 ( 5621) covalent geometry : angle 0.65094 ( 7644) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 0.626 Fit side-chains REVERT: A 43 GLN cc_start: 0.8475 (mm-40) cc_final: 0.7964 (mp10) REVERT: A 46 GLU cc_start: 0.8771 (tt0) cc_final: 0.8518 (tt0) REVERT: A 89 ASP cc_start: 0.8333 (m-30) cc_final: 0.7482 (t0) REVERT: B 24 ARG cc_start: 0.7602 (tpp-160) cc_final: 0.7394 (tpp-160) REVERT: B 62 ARG cc_start: 0.8315 (ptt-90) cc_final: 0.8079 (ptp-170) REVERT: B 117 ILE cc_start: 0.6792 (tt) cc_final: 0.6421 (mm) REVERT: B 166 GLN cc_start: 0.7188 (tt0) cc_final: 0.6760 (tt0) REVERT: M 403 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7042 (ttt-90) REVERT: M 461 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7529 (pp) REVERT: M 465 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8100 (tt0) REVERT: M 574 ASP cc_start: 0.8155 (p0) cc_final: 0.7652 (p0) REVERT: M 586 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8104 (m-30) outliers start: 21 outliers final: 12 residues processed: 73 average time/residue: 1.2295 time to fit residues: 94.0652 Evaluate side-chains 72 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 345 THR Chi-restraints excluded: chain M residue 403 ARG Chi-restraints excluded: chain M residue 461 LEU Chi-restraints excluded: chain M residue 465 GLU Chi-restraints excluded: chain M residue 553 THR Chi-restraints excluded: chain M residue 572 THR Chi-restraints excluded: chain M residue 581 THR Chi-restraints excluded: chain M residue 586 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.3980 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 37 optimal weight: 0.4980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4185 r_free = 0.4185 target = 0.184653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.121788 restraints weight = 6120.280| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.43 r_work: 0.3347 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5632 Z= 0.149 Angle : 0.668 13.216 7669 Z= 0.339 Chirality : 0.047 0.322 858 Planarity : 0.006 0.065 981 Dihedral : 4.975 20.761 823 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.96 % Allowed : 16.61 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.32), residues: 696 helix: -4.20 (0.57), residues: 26 sheet: 0.60 (0.33), residues: 262 loop : -1.06 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 47 HIS 0.005 0.001 HIS B 92 PHE 0.017 0.001 PHE M 377 TYR 0.008 0.001 TYR B 37 ARG 0.007 0.000 ARG B 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 1) link_NAG-ASN : angle 1.50562 ( 3) link_BETA1-4 : bond 0.00193 ( 1) link_BETA1-4 : angle 2.28259 ( 3) hydrogen bonds : bond 0.03493 ( 181) hydrogen bonds : angle 5.40467 ( 513) link_BETA1-6 : bond 0.00079 ( 1) link_BETA1-6 : angle 1.51547 ( 3) SS BOND : bond 0.01192 ( 8) SS BOND : angle 2.61360 ( 16) covalent geometry : bond 0.00352 ( 5621) covalent geometry : angle 0.65581 ( 7644) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.618 Fit side-chains REVERT: A 43 GLN cc_start: 0.8481 (mm-40) cc_final: 0.7968 (mp10) REVERT: A 46 GLU cc_start: 0.8735 (tt0) cc_final: 0.8512 (tt0) REVERT: A 89 ASP cc_start: 0.8323 (m-30) cc_final: 0.7489 (t0) REVERT: B 117 ILE cc_start: 0.6809 (tt) cc_final: 0.6422 (mm) REVERT: M 357 ARG cc_start: 0.8909 (ttp-170) cc_final: 0.8503 (ttp80) REVERT: M 403 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7012 (ttt-90) REVERT: M 461 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7460 (pp) REVERT: M 465 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8045 (tt0) REVERT: M 586 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8109 (m-30) outliers start: 18 outliers final: 9 residues processed: 69 average time/residue: 1.2447 time to fit residues: 90.1164 Evaluate side-chains 70 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 345 THR Chi-restraints excluded: chain M residue 403 ARG Chi-restraints excluded: chain M residue 461 LEU Chi-restraints excluded: chain M residue 465 GLU Chi-restraints excluded: chain M residue 572 THR Chi-restraints excluded: chain M residue 581 THR Chi-restraints excluded: chain M residue 586 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 37 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.4185 r_free = 0.4185 target = 0.184591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.121653 restraints weight = 6091.922| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.43 r_work: 0.3347 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5632 Z= 0.153 Angle : 0.677 14.919 7669 Z= 0.344 Chirality : 0.047 0.291 858 Planarity : 0.006 0.065 981 Dihedral : 5.013 27.317 823 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.12 % Allowed : 16.78 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.32), residues: 696 helix: -4.21 (0.58), residues: 26 sheet: 0.58 (0.33), residues: 261 loop : -1.08 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 47 HIS 0.005 0.001 HIS B 92 PHE 0.019 0.001 PHE M 377 TYR 0.011 0.001 TYR M 380 ARG 0.008 0.000 ARG B 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00515 ( 1) link_NAG-ASN : angle 1.47406 ( 3) link_BETA1-4 : bond 0.00231 ( 1) link_BETA1-4 : angle 2.28214 ( 3) hydrogen bonds : bond 0.03507 ( 181) hydrogen bonds : angle 5.39813 ( 513) link_BETA1-6 : bond 0.00062 ( 1) link_BETA1-6 : angle 1.50905 ( 3) SS BOND : bond 0.01115 ( 8) SS BOND : angle 1.97258 ( 16) covalent geometry : bond 0.00363 ( 5621) covalent geometry : angle 0.66937 ( 7644) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.940 Fit side-chains REVERT: A 43 GLN cc_start: 0.8480 (mm-40) cc_final: 0.7963 (mp10) REVERT: A 46 GLU cc_start: 0.8736 (tt0) cc_final: 0.8509 (tt0) REVERT: A 89 ASP cc_start: 0.8323 (m-30) cc_final: 0.7484 (t0) REVERT: B 117 ILE cc_start: 0.6798 (tt) cc_final: 0.6401 (mm) REVERT: M 357 ARG cc_start: 0.8923 (ttp-170) cc_final: 0.8513 (ttp80) REVERT: M 403 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7028 (ttt-90) REVERT: M 461 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7473 (pp) REVERT: M 465 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8047 (tt0) REVERT: M 574 ASP cc_start: 0.8095 (p0) cc_final: 0.7736 (p0) REVERT: M 586 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.8119 (m-30) outliers start: 19 outliers final: 12 residues processed: 70 average time/residue: 1.1932 time to fit residues: 87.4907 Evaluate side-chains 71 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 345 THR Chi-restraints excluded: chain M residue 403 ARG Chi-restraints excluded: chain M residue 461 LEU Chi-restraints excluded: chain M residue 465 GLU Chi-restraints excluded: chain M residue 572 THR Chi-restraints excluded: chain M residue 581 THR Chi-restraints excluded: chain M residue 586 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 8 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 34 optimal weight: 0.0370 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 52 optimal weight: 0.4980 chunk 51 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.4460 ------------------------------------------------------------------------------- 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 = 0.4212 r_free = 0.4212 target = 0.187298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.125011 restraints weight = 6070.186| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.44 r_work: 0.3386 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5632 Z= 0.104 Angle : 0.619 11.981 7669 Z= 0.312 Chirality : 0.045 0.238 858 Planarity : 0.005 0.062 981 Dihedral : 4.662 26.675 823 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.63 % Allowed : 16.94 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.32), residues: 696 helix: -4.13 (0.62), residues: 26 sheet: 0.59 (0.33), residues: 264 loop : -1.00 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 47 HIS 0.004 0.001 HIS B 92 PHE 0.015 0.001 PHE M 429 TYR 0.008 0.001 TYR M 380 ARG 0.009 0.001 ARG B 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 1) link_NAG-ASN : angle 1.54942 ( 3) link_BETA1-4 : bond 0.00334 ( 1) link_BETA1-4 : angle 1.92039 ( 3) hydrogen bonds : bond 0.03010 ( 181) hydrogen bonds : angle 5.23832 ( 513) link_BETA1-6 : bond 0.00089 ( 1) link_BETA1-6 : angle 1.39642 ( 3) SS BOND : bond 0.00831 ( 8) SS BOND : angle 1.27926 ( 16) covalent geometry : bond 0.00235 ( 5621) covalent geometry : angle 0.61472 ( 7644) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.611 Fit side-chains REVERT: A 43 GLN cc_start: 0.8382 (mm-40) cc_final: 0.7873 (mp10) REVERT: A 89 ASP cc_start: 0.8315 (m-30) cc_final: 0.7502 (t0) REVERT: A 138 LEU cc_start: 0.5660 (OUTLIER) cc_final: 0.5152 (pp) REVERT: B 83 ASP cc_start: 0.8151 (m-30) cc_final: 0.7757 (m-30) REVERT: B 117 ILE cc_start: 0.6756 (tt) cc_final: 0.6360 (mm) REVERT: M 357 ARG cc_start: 0.8910 (ttp-170) cc_final: 0.8501 (ttp80) REVERT: M 403 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.6909 (ttt-90) REVERT: M 461 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7219 (pp) REVERT: M 489 TYR cc_start: 0.7495 (m-80) cc_final: 0.7196 (m-80) REVERT: M 574 ASP cc_start: 0.8046 (p0) cc_final: 0.7679 (p0) REVERT: M 586 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.8101 (m-30) outliers start: 16 outliers final: 10 residues processed: 72 average time/residue: 1.1905 time to fit residues: 89.8921 Evaluate side-chains 70 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 403 ARG Chi-restraints excluded: chain M residue 461 LEU Chi-restraints excluded: chain M residue 572 THR Chi-restraints excluded: chain M residue 581 THR Chi-restraints excluded: chain M residue 586 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 41 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 40 optimal weight: 0.2980 chunk 18 optimal weight: 4.9990 chunk 44 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 11 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.185497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.122837 restraints weight = 6088.361| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.42 r_work: 0.3360 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5632 Z= 0.138 Angle : 0.647 12.475 7669 Z= 0.327 Chirality : 0.046 0.251 858 Planarity : 0.006 0.059 981 Dihedral : 4.779 27.956 823 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.47 % Allowed : 18.09 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.32), residues: 696 helix: -4.14 (0.61), residues: 26 sheet: 0.55 (0.33), residues: 264 loop : -1.01 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 47 HIS 0.004 0.001 HIS B 92 PHE 0.013 0.001 PHE M 377 TYR 0.008 0.001 TYR A 159 ARG 0.008 0.000 ARG B 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00511 ( 1) link_NAG-ASN : angle 1.48834 ( 3) link_BETA1-4 : bond 0.00191 ( 1) link_BETA1-4 : angle 2.16352 ( 3) hydrogen bonds : bond 0.03300 ( 181) hydrogen bonds : angle 5.29003 ( 513) link_BETA1-6 : bond 0.00100 ( 1) link_BETA1-6 : angle 1.43476 ( 3) SS BOND : bond 0.01030 ( 8) SS BOND : angle 1.53448 ( 16) covalent geometry : bond 0.00326 ( 5621) covalent geometry : angle 0.64116 ( 7644) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.540 Fit side-chains REVERT: A 43 GLN cc_start: 0.8442 (mm-40) cc_final: 0.7908 (mp10) REVERT: A 89 ASP cc_start: 0.8316 (m-30) cc_final: 0.7502 (t0) REVERT: B 78 ARG cc_start: 0.6788 (ttp-110) cc_final: 0.6574 (ttp-110) REVERT: M 403 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.6980 (ttt-90) REVERT: M 461 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7448 (pp) REVERT: M 489 TYR cc_start: 0.7509 (m-80) cc_final: 0.7210 (m-80) REVERT: M 574 ASP cc_start: 0.8068 (p0) cc_final: 0.7695 (p0) REVERT: M 586 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8124 (m-30) outliers start: 15 outliers final: 11 residues processed: 67 average time/residue: 1.1767 time to fit residues: 82.5798 Evaluate side-chains 67 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 403 ARG Chi-restraints excluded: chain M residue 461 LEU Chi-restraints excluded: chain M residue 572 THR Chi-restraints excluded: chain M residue 581 THR Chi-restraints excluded: chain M residue 586 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.185752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.123051 restraints weight = 6128.084| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.44 r_work: 0.3365 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5632 Z= 0.130 Angle : 0.649 12.752 7669 Z= 0.325 Chirality : 0.046 0.241 858 Planarity : 0.005 0.059 981 Dihedral : 4.764 27.836 823 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.30 % Allowed : 18.26 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.32), residues: 696 helix: -4.14 (0.61), residues: 26 sheet: 0.56 (0.33), residues: 264 loop : -0.98 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 47 HIS 0.004 0.001 HIS B 92 PHE 0.013 0.001 PHE M 377 TYR 0.007 0.001 TYR A 159 ARG 0.008 0.000 ARG B 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 1) link_NAG-ASN : angle 1.49024 ( 3) link_BETA1-4 : bond 0.00197 ( 1) link_BETA1-4 : angle 2.09564 ( 3) hydrogen bonds : bond 0.03230 ( 181) hydrogen bonds : angle 5.28071 ( 513) link_BETA1-6 : bond 0.00031 ( 1) link_BETA1-6 : angle 1.46291 ( 3) SS BOND : bond 0.00994 ( 8) SS BOND : angle 1.36734 ( 16) covalent geometry : bond 0.00303 ( 5621) covalent geometry : angle 0.64426 ( 7644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7274.51 seconds wall clock time: 129 minutes 11.84 seconds (7751.84 seconds total)