Starting phenix.real_space_refine on Wed Feb 12 22:15:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kej_37160/02_2025/8kej_37160.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kej_37160/02_2025/8kej_37160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kej_37160/02_2025/8kej_37160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kej_37160/02_2025/8kej_37160.map" model { file = "/net/cci-nas-00/data/ceres_data/8kej_37160/02_2025/8kej_37160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kej_37160/02_2025/8kej_37160.cif" } resolution = 3.73 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= 0.002 sd= 0.031 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: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 5332 2.51 5 N 1394 2.21 5 O 1616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8377 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1638 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "L" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1653 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 12, 'TRANS': 200} Chain: "A" Number of atoms: 5086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5086 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 33, 'TRANS': 610} Chain breaks: 2 Time building chain proxies: 4.99, per 1000 atoms: 0.60 Number of scatterers: 8377 At special positions: 0 Unit cell: (93.2, 115.568, 157.508, 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 35 16.00 O 1616 8.00 N 1394 7.00 C 5332 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " 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 Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 965.4 milliseconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2006 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 22 sheets defined 4.1% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'H' and resid 134 through 138 removed outlier: 4.126A pdb=" N THR H 138 " --> pdb=" O SER H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 165 No H-bonds generated for 'chain 'H' and resid 163 through 165' Processing helix chain 'H' and resid 194 through 196 No H-bonds generated for 'chain 'H' and resid 194 through 196' Processing helix chain 'L' and resid 123 through 129 removed outlier: 3.659A pdb=" N SER L 129 " --> pdb=" O GLU L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 191 removed outlier: 3.695A pdb=" N HIS L 191 " --> pdb=" O ASP L 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.690A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.604A pdb=" N LEU H 83 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 9 through 12 removed outlier: 6.840A pdb=" N GLU H 10 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET H 34 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL H 50 " --> pdb=" O THR H 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 127 through 131 Processing sheet with id=AA4, first strand: chain 'H' and resid 160 through 161 Processing sheet with id=AA5, first strand: chain 'H' and resid 176 through 177 Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.568A pdb=" N LEU L 13 " --> pdb=" O GLU L 107 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 20 through 22 removed outlier: 3.797A pdb=" N LEU L 21 " --> pdb=" O LEU L 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 45 through 49 removed outlier: 5.583A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 116 through 120 removed outlier: 5.979A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 155 through 157 removed outlier: 4.349A pdb=" N TRP L 150 " --> pdb=" O GLN L 157 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS L 147 " --> pdb=" O THR L 199 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR L 199 " --> pdb=" O LYS L 147 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.832A pdb=" N ALA A 263 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 49 through 56 removed outlier: 4.213A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 71 through 72 removed outlier: 3.609A pdb=" N VAL A 71 " --> pdb=" O ARG A 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.669A pdb=" N ARG A 190 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.949A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 166 through 170 removed outlier: 3.536A pdb=" N PHE A 168 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE A 129 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP A 105 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.609A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AC1, first strand: chain 'A' and resid 541 through 543 removed outlier: 3.794A pdb=" N LEU A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 551 through 554 Processing sheet with id=AC3, first strand: chain 'A' and resid 594 through 598 Processing sheet with id=AC4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.964A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) 182 hydrogen bonds defined for protein. 471 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 2.34 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: 2594 1.34 - 1.45: 1450 1.45 - 1.57: 4501 1.57 - 1.69: 0 1.69 - 1.81: 43 Bond restraints: 8588 Sorted by residual: bond pdb=" N GLU L 145 " pdb=" CA GLU L 145 " ideal model delta sigma weight residual 1.459 1.488 -0.028 9.10e-03 1.21e+04 9.65e+00 bond pdb=" N VAL A 595 " pdb=" CA VAL A 595 " ideal model delta sigma weight residual 1.460 1.493 -0.034 1.10e-02 8.26e+03 9.42e+00 bond pdb=" N ASN L 139 " pdb=" CA ASN L 139 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.23e-02 6.61e+03 8.76e+00 bond pdb=" N LEU A 585 " pdb=" CA LEU A 585 " ideal model delta sigma weight residual 1.455 1.489 -0.035 1.25e-02 6.40e+03 7.65e+00 bond pdb=" N ARG L 144 " pdb=" CA ARG L 144 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.96e+00 ... (remaining 8583 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 10981 1.24 - 2.49: 542 2.49 - 3.73: 137 3.73 - 4.98: 22 4.98 - 6.22: 7 Bond angle restraints: 11689 Sorted by residual: angle pdb=" CA PHE L 141 " pdb=" CB PHE L 141 " pdb=" CG PHE L 141 " ideal model delta sigma weight residual 113.80 117.84 -4.04 1.00e+00 1.00e+00 1.64e+01 angle pdb=" N GLU L 145 " pdb=" CA GLU L 145 " pdb=" C GLU L 145 " ideal model delta sigma weight residual 112.99 106.78 6.21 1.61e+00 3.86e-01 1.49e+01 angle pdb=" C TYR L 142 " pdb=" N PRO L 143 " pdb=" CA PRO L 143 " ideal model delta sigma weight residual 119.84 124.53 -4.69 1.25e+00 6.40e-01 1.41e+01 angle pdb=" C PHE H 102 " pdb=" N ILE H 103 " pdb=" CA ILE H 103 " ideal model delta sigma weight residual 120.43 123.97 -3.54 9.60e-01 1.09e+00 1.36e+01 angle pdb=" CA TYR L 142 " pdb=" C TYR L 142 " pdb=" O TYR L 142 " ideal model delta sigma weight residual 120.87 116.94 3.93 1.10e+00 8.26e-01 1.28e+01 ... (remaining 11684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 4840 17.31 - 34.63: 212 34.63 - 51.94: 39 51.94 - 69.25: 9 69.25 - 86.56: 1 Dihedral angle restraints: 5101 sinusoidal: 1970 harmonic: 3131 Sorted by residual: dihedral pdb=" CA PRO A 589 " pdb=" C PRO A 589 " pdb=" N CYS A 590 " pdb=" CA CYS A 590 " ideal model delta harmonic sigma weight residual 180.00 -155.63 -24.37 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CB GLU A 281 " pdb=" CG GLU A 281 " pdb=" CD GLU A 281 " pdb=" OE1 GLU A 281 " ideal model delta sinusoidal sigma weight residual 0.00 86.56 -86.56 1 3.00e+01 1.11e-03 1.00e+01 dihedral pdb=" CG ARG L 144 " pdb=" CD ARG L 144 " pdb=" NE ARG L 144 " pdb=" CZ ARG L 144 " ideal model delta sinusoidal sigma weight residual -180.00 -136.73 -43.27 2 1.50e+01 4.44e-03 1.00e+01 ... (remaining 5098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1087 0.055 - 0.110: 197 0.110 - 0.165: 15 0.165 - 0.220: 2 0.220 - 0.275: 1 Chirality restraints: 1302 Sorted by residual: chirality pdb=" CA LEU A 585 " pdb=" N LEU A 585 " pdb=" C LEU A 585 " pdb=" CB LEU A 585 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA GLU L 145 " pdb=" N GLU L 145 " pdb=" C GLU L 145 " pdb=" CB GLU L 145 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.34e-01 chirality pdb=" CA LYS L 147 " pdb=" N LYS L 147 " pdb=" C LYS L 147 " pdb=" CB LYS L 147 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.44e-01 ... (remaining 1299 not shown) Planarity restraints: 1507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO A 521 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 462 " 0.019 5.00e-02 4.00e+02 2.89e-02 1.33e+00 pdb=" N PRO A 463 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 329 " -0.019 5.00e-02 4.00e+02 2.81e-02 1.27e+00 pdb=" N PRO A 330 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 330 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 330 " -0.016 5.00e-02 4.00e+02 ... (remaining 1504 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1685 2.78 - 3.31: 7447 3.31 - 3.84: 13495 3.84 - 4.37: 15093 4.37 - 4.90: 26493 Nonbonded interactions: 64213 Sorted by model distance: nonbonded pdb=" OE1 GLU L 107 " pdb=" OH TYR L 175 " model vdw 2.252 3.040 nonbonded pdb=" OG1 THR A 430 " pdb=" O PHE A 515 " model vdw 2.277 3.040 nonbonded pdb=" OH TYR L 32 " pdb=" OD1 ASP A 428 " model vdw 2.283 3.040 nonbonded pdb=" O VAL H 149 " pdb=" OG SER H 184 " model vdw 2.291 3.040 nonbonded pdb=" O TYR L 188 " pdb=" OH TYR L 194 " model vdw 2.299 3.040 ... (remaining 64208 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.370 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5604 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8588 Z= 0.191 Angle : 0.653 6.219 11689 Z= 0.417 Chirality : 0.042 0.275 1302 Planarity : 0.003 0.033 1507 Dihedral : 9.634 86.563 3059 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.70 % Favored : 92.11 % Rotamer: Outliers : 5.75 % Allowed : 7.35 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.21 (0.21), residues: 1065 helix: -2.47 (0.70), residues: 31 sheet: -2.40 (0.25), residues: 322 loop : -3.20 (0.19), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP A 353 HIS 0.001 0.000 HIS L 90 PHE 0.018 0.001 PHE L 141 TYR 0.007 0.001 TYR L 142 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 228 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 59 THR cc_start: 0.8256 (m) cc_final: 0.7505 (p) REVERT: H 85 SER cc_start: 0.7685 (t) cc_final: 0.7411 (p) REVERT: H 91 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8517 (p) REVERT: H 117 LEU cc_start: 0.8193 (tp) cc_final: 0.7982 (tp) REVERT: H 176 VAL cc_start: 0.7815 (t) cc_final: 0.7526 (p) REVERT: H 200 THR cc_start: 0.8462 (m) cc_final: 0.8140 (t) REVERT: H 201 TYR cc_start: 0.6469 (m-80) cc_final: 0.6173 (m-80) REVERT: L 120 PHE cc_start: 0.7454 (m-80) cc_final: 0.7248 (m-80) REVERT: L 164 SER cc_start: 0.8213 (t) cc_final: 0.7648 (p) REVERT: L 171 LYS cc_start: 0.8395 (mttt) cc_final: 0.8190 (mttt) REVERT: L 178 SER cc_start: 0.8267 (t) cc_final: 0.8028 (p) REVERT: A 57 LEU cc_start: 0.7331 (tp) cc_final: 0.7046 (tp) REVERT: A 203 ILE cc_start: 0.6012 (mt) cc_final: 0.5713 (mm) REVERT: A 357 ARG cc_start: 0.7519 (ptm-80) cc_final: 0.7279 (ptm-80) REVERT: A 359 SER cc_start: 0.7902 (p) cc_final: 0.7655 (p) REVERT: A 436 TRP cc_start: 0.7417 (p90) cc_final: 0.6776 (p90) REVERT: A 448 ASN cc_start: 0.6863 (m110) cc_final: 0.6514 (m-40) REVERT: A 460 LYS cc_start: 0.7776 (mptm) cc_final: 0.7525 (mptm) REVERT: A 510 VAL cc_start: 0.8205 (t) cc_final: 0.7817 (m) REVERT: A 511 VAL cc_start: 0.7851 (OUTLIER) cc_final: 0.7488 (m) REVERT: A 524 VAL cc_start: 0.5265 (OUTLIER) cc_final: 0.4634 (t) REVERT: A 585 LEU cc_start: 0.5688 (OUTLIER) cc_final: 0.5278 (pp) REVERT: A 592 PHE cc_start: 0.0518 (OUTLIER) cc_final: -0.0528 (m-80) outliers start: 54 outliers final: 19 residues processed: 267 average time/residue: 0.2344 time to fit residues: 84.0031 Evaluate side-chains 227 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 124 LYS Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 677 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 0.0370 chunk 42 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 96 optimal weight: 0.0010 overall best weight: 0.7866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 114 GLN H 171 HIS L 38 GLN L 42 GLN L 102 GLN L 168 GLN A 53 GLN A 173 GLN A 354 ASN A 409 GLN A 414 GLN A 422 ASN A 450 ASN A 487 ASN A 613 GLN A 675 GLN A 677 GLN A 690 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.218450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.184226 restraints weight = 18342.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.189666 restraints weight = 9623.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.193109 restraints weight = 5761.200| |-----------------------------------------------------------------------------| r_work (final): 0.4377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5754 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 8588 Z= 0.220 Angle : 0.607 10.588 11689 Z= 0.311 Chirality : 0.045 0.168 1302 Planarity : 0.005 0.055 1507 Dihedral : 7.084 87.745 1217 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 4.69 % Allowed : 12.46 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.54 (0.22), residues: 1065 helix: -1.49 (0.87), residues: 25 sheet: -1.76 (0.27), residues: 318 loop : -2.84 (0.20), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 94 HIS 0.003 0.001 HIS A 245 PHE 0.017 0.001 PHE A 377 TYR 0.017 0.001 TYR A 265 ARG 0.003 0.000 ARG L 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 217 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.7770 (mp) cc_final: 0.7024 (tt) REVERT: H 29 PHE cc_start: 0.8010 (t80) cc_final: 0.7810 (t80) REVERT: H 68 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8051 (t) REVERT: H 85 SER cc_start: 0.7734 (t) cc_final: 0.7298 (p) REVERT: H 103 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.6141 (mt) REVERT: H 117 LEU cc_start: 0.8204 (tp) cc_final: 0.7989 (tp) REVERT: H 148 LEU cc_start: 0.8093 (tt) cc_final: 0.7861 (tt) REVERT: H 160 SER cc_start: 0.8011 (p) cc_final: 0.7721 (t) REVERT: H 176 VAL cc_start: 0.7688 (t) cc_final: 0.7250 (p) REVERT: H 189 VAL cc_start: 0.8654 (t) cc_final: 0.8263 (p) REVERT: H 200 THR cc_start: 0.8519 (m) cc_final: 0.8172 (t) REVERT: H 201 TYR cc_start: 0.6454 (m-80) cc_final: 0.6160 (m-80) REVERT: L 11 LEU cc_start: 0.7595 (tp) cc_final: 0.7355 (mm) REVERT: L 14 SER cc_start: 0.8131 (t) cc_final: 0.7915 (m) REVERT: L 46 LEU cc_start: 0.8044 (tp) cc_final: 0.7727 (tp) REVERT: L 82 ASP cc_start: 0.8199 (m-30) cc_final: 0.7989 (m-30) REVERT: L 83 PHE cc_start: 0.7536 (m-80) cc_final: 0.7147 (m-80) REVERT: L 97 MET cc_start: 0.6241 (mtm) cc_final: 0.5729 (mtm) REVERT: L 164 SER cc_start: 0.8396 (t) cc_final: 0.7979 (p) REVERT: L 171 LYS cc_start: 0.8481 (mttt) cc_final: 0.8263 (mttt) REVERT: L 178 SER cc_start: 0.8297 (t) cc_final: 0.7412 (m) REVERT: A 57 LEU cc_start: 0.7395 (tp) cc_final: 0.7104 (tp) REVERT: A 59 PHE cc_start: 0.7176 (m-10) cc_final: 0.6972 (m-10) REVERT: A 147 LYS cc_start: 0.4538 (mmmt) cc_final: 0.4328 (mmmt) REVERT: A 269 TYR cc_start: 0.7557 (m-80) cc_final: 0.7319 (m-80) REVERT: A 298 GLU cc_start: 0.7283 (tt0) cc_final: 0.7082 (tt0) REVERT: A 310 LYS cc_start: 0.7364 (mtmt) cc_final: 0.6832 (ptpp) REVERT: A 357 ARG cc_start: 0.7536 (ptm-80) cc_final: 0.7274 (ptm-80) REVERT: A 378 LYS cc_start: 0.8039 (ptpp) cc_final: 0.7577 (pttm) REVERT: A 382 VAL cc_start: 0.5914 (OUTLIER) cc_final: 0.4985 (p) REVERT: A 436 TRP cc_start: 0.7233 (p90) cc_final: 0.6793 (p90) REVERT: A 448 ASN cc_start: 0.6987 (m110) cc_final: 0.6615 (m-40) REVERT: A 460 LYS cc_start: 0.8164 (mptm) cc_final: 0.7713 (mptm) REVERT: A 510 VAL cc_start: 0.8179 (t) cc_final: 0.7943 (m) REVERT: A 542 ASN cc_start: 0.6932 (t0) cc_final: 0.6694 (t0) REVERT: A 592 PHE cc_start: 0.1047 (OUTLIER) cc_final: -0.0479 (m-10) REVERT: A 697 MET cc_start: -0.4682 (ptp) cc_final: -0.5686 (ptt) outliers start: 44 outliers final: 27 residues processed: 251 average time/residue: 0.2213 time to fit residues: 74.6156 Evaluate side-chains 232 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 124 LYS Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 142 TYR Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 596 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 65 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 98 optimal weight: 0.0670 chunk 94 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 107 ASN H 171 HIS ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.216630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.182075 restraints weight = 18553.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.187616 restraints weight = 9769.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.191087 restraints weight = 5856.916| |-----------------------------------------------------------------------------| r_work (final): 0.4359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5818 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8588 Z= 0.203 Angle : 0.581 10.228 11689 Z= 0.300 Chirality : 0.045 0.175 1302 Planarity : 0.004 0.052 1507 Dihedral : 6.953 87.808 1206 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 4.47 % Allowed : 14.80 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.24 (0.23), residues: 1065 helix: -1.85 (0.77), residues: 26 sheet: -1.47 (0.28), residues: 338 loop : -2.68 (0.21), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP L 150 HIS 0.002 0.001 HIS L 200 PHE 0.018 0.002 PHE H 129 TYR 0.014 0.001 TYR A 265 ARG 0.003 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 202 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.7811 (mp) cc_final: 0.6917 (tt) REVERT: H 29 PHE cc_start: 0.8052 (t80) cc_final: 0.7841 (t80) REVERT: H 36 TRP cc_start: 0.7180 (t-100) cc_final: 0.6690 (m-90) REVERT: H 85 SER cc_start: 0.7722 (t) cc_final: 0.7234 (p) REVERT: H 148 LEU cc_start: 0.8058 (tt) cc_final: 0.7846 (tt) REVERT: H 160 SER cc_start: 0.8015 (p) cc_final: 0.7780 (t) REVERT: H 176 VAL cc_start: 0.7851 (t) cc_final: 0.7427 (p) REVERT: H 189 VAL cc_start: 0.8635 (t) cc_final: 0.8227 (p) REVERT: H 200 THR cc_start: 0.8535 (m) cc_final: 0.8175 (t) REVERT: H 201 TYR cc_start: 0.6441 (m-80) cc_final: 0.6144 (m-80) REVERT: L 14 SER cc_start: 0.8221 (t) cc_final: 0.8008 (m) REVERT: L 46 LEU cc_start: 0.8121 (tp) cc_final: 0.7835 (tp) REVERT: L 83 PHE cc_start: 0.7576 (m-80) cc_final: 0.7195 (m-80) REVERT: L 97 MET cc_start: 0.6274 (mtm) cc_final: 0.5872 (mtm) REVERT: L 164 SER cc_start: 0.8393 (t) cc_final: 0.8050 (p) REVERT: L 178 SER cc_start: 0.8293 (t) cc_final: 0.7366 (m) REVERT: A 57 LEU cc_start: 0.7488 (tp) cc_final: 0.7105 (tp) REVERT: A 59 PHE cc_start: 0.7167 (m-10) cc_final: 0.6926 (m-10) REVERT: A 269 TYR cc_start: 0.7641 (m-80) cc_final: 0.7384 (m-80) REVERT: A 298 GLU cc_start: 0.7379 (tt0) cc_final: 0.7132 (tt0) REVERT: A 310 LYS cc_start: 0.7487 (mtmt) cc_final: 0.7219 (mtpt) REVERT: A 357 ARG cc_start: 0.7636 (ptm-80) cc_final: 0.7199 (ptm-80) REVERT: A 369 TYR cc_start: 0.7251 (m-80) cc_final: 0.7043 (m-10) REVERT: A 378 LYS cc_start: 0.8121 (ptpp) cc_final: 0.7776 (ptpp) REVERT: A 382 VAL cc_start: 0.5977 (OUTLIER) cc_final: 0.5040 (p) REVERT: A 394 ASN cc_start: 0.6339 (t0) cc_final: 0.5762 (t0) REVERT: A 406 GLU cc_start: 0.7466 (pt0) cc_final: 0.7140 (pt0) REVERT: A 424 LYS cc_start: 0.8040 (ttmm) cc_final: 0.7803 (ttmm) REVERT: A 436 TRP cc_start: 0.7279 (p90) cc_final: 0.6803 (p90) REVERT: A 438 SER cc_start: 0.8188 (p) cc_final: 0.7749 (t) REVERT: A 448 ASN cc_start: 0.7073 (m110) cc_final: 0.6700 (m-40) REVERT: A 460 LYS cc_start: 0.8234 (mptm) cc_final: 0.7769 (mptm) REVERT: A 465 GLU cc_start: 0.6957 (tt0) cc_final: 0.6394 (tt0) REVERT: A 510 VAL cc_start: 0.8195 (t) cc_final: 0.7966 (m) REVERT: A 539 VAL cc_start: 0.7710 (t) cc_final: 0.7459 (p) REVERT: A 542 ASN cc_start: 0.6852 (t0) cc_final: 0.6600 (t0) REVERT: A 592 PHE cc_start: 0.1265 (OUTLIER) cc_final: -0.0518 (m-80) REVERT: A 697 MET cc_start: -0.4776 (ptp) cc_final: -0.5682 (ptt) outliers start: 42 outliers final: 31 residues processed: 231 average time/residue: 0.2232 time to fit residues: 69.3727 Evaluate side-chains 229 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 124 LYS Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 142 TYR Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 596 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 0 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 4 optimal weight: 0.5980 chunk 89 optimal weight: 0.5980 chunk 103 optimal weight: 0.0470 chunk 17 optimal weight: 0.5980 chunk 14 optimal weight: 10.0000 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 171 HIS A 207 HIS A 314 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.216230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.182281 restraints weight = 18361.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.187764 restraints weight = 9702.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.191189 restraints weight = 5818.985| |-----------------------------------------------------------------------------| r_work (final): 0.4348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5816 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8588 Z= 0.170 Angle : 0.554 9.238 11689 Z= 0.281 Chirality : 0.044 0.182 1302 Planarity : 0.004 0.054 1507 Dihedral : 6.920 87.729 1205 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 4.69 % Allowed : 15.97 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.99 (0.24), residues: 1065 helix: -1.16 (0.87), residues: 26 sheet: -1.27 (0.28), residues: 341 loop : -2.54 (0.21), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 150 HIS 0.003 0.001 HIS L 191 PHE 0.015 0.001 PHE A 60 TYR 0.013 0.001 TYR A 265 ARG 0.004 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.7796 (mp) cc_final: 0.7165 (tt) REVERT: H 29 PHE cc_start: 0.8024 (t80) cc_final: 0.7814 (t80) REVERT: H 34 MET cc_start: 0.7447 (mmm) cc_final: 0.7097 (mmm) REVERT: H 36 TRP cc_start: 0.7220 (t-100) cc_final: 0.6728 (m-90) REVERT: H 52 ASN cc_start: 0.8187 (t0) cc_final: 0.7942 (t0) REVERT: H 68 VAL cc_start: 0.8515 (OUTLIER) cc_final: 0.8262 (t) REVERT: H 85 SER cc_start: 0.7512 (t) cc_final: 0.7057 (p) REVERT: H 117 LEU cc_start: 0.8238 (tp) cc_final: 0.8011 (tp) REVERT: H 160 SER cc_start: 0.8061 (p) cc_final: 0.7776 (t) REVERT: H 172 THR cc_start: 0.8501 (m) cc_final: 0.7876 (p) REVERT: H 176 VAL cc_start: 0.7823 (t) cc_final: 0.7426 (p) REVERT: H 189 VAL cc_start: 0.8548 (t) cc_final: 0.8188 (p) REVERT: H 200 THR cc_start: 0.8516 (m) cc_final: 0.8177 (t) REVERT: H 201 TYR cc_start: 0.6407 (m-80) cc_final: 0.6131 (m-80) REVERT: L 46 LEU cc_start: 0.8161 (tp) cc_final: 0.7903 (tp) REVERT: L 83 PHE cc_start: 0.7484 (m-80) cc_final: 0.7113 (m-80) REVERT: L 97 MET cc_start: 0.6246 (mtm) cc_final: 0.5931 (mtm) REVERT: L 164 SER cc_start: 0.8375 (t) cc_final: 0.8103 (p) REVERT: L 178 SER cc_start: 0.8325 (t) cc_final: 0.7416 (m) REVERT: A 59 PHE cc_start: 0.7137 (m-10) cc_final: 0.6906 (m-10) REVERT: A 269 TYR cc_start: 0.7574 (m-80) cc_final: 0.7315 (m-80) REVERT: A 298 GLU cc_start: 0.7331 (tt0) cc_final: 0.7085 (tt0) REVERT: A 353 TRP cc_start: 0.8071 (p-90) cc_final: 0.7538 (p-90) REVERT: A 357 ARG cc_start: 0.7616 (ptm-80) cc_final: 0.7259 (ptm-80) REVERT: A 369 TYR cc_start: 0.7269 (m-80) cc_final: 0.7048 (m-10) REVERT: A 378 LYS cc_start: 0.8061 (ptpp) cc_final: 0.7768 (ptpp) REVERT: A 382 VAL cc_start: 0.6026 (OUTLIER) cc_final: 0.5082 (p) REVERT: A 406 GLU cc_start: 0.7489 (pt0) cc_final: 0.7252 (pt0) REVERT: A 424 LYS cc_start: 0.7990 (ttmm) cc_final: 0.7730 (ttmm) REVERT: A 436 TRP cc_start: 0.7321 (p90) cc_final: 0.6773 (p90) REVERT: A 448 ASN cc_start: 0.7057 (m110) cc_final: 0.6697 (m-40) REVERT: A 460 LYS cc_start: 0.8247 (mptm) cc_final: 0.7813 (mptm) REVERT: A 465 GLU cc_start: 0.6964 (tt0) cc_final: 0.6403 (tt0) REVERT: A 493 GLN cc_start: 0.6168 (tp40) cc_final: 0.5783 (tp40) REVERT: A 510 VAL cc_start: 0.8086 (t) cc_final: 0.7846 (m) REVERT: A 539 VAL cc_start: 0.7746 (t) cc_final: 0.7523 (p) REVERT: A 542 ASN cc_start: 0.6947 (t0) cc_final: 0.6687 (t0) REVERT: A 592 PHE cc_start: 0.1367 (OUTLIER) cc_final: -0.0032 (m-10) REVERT: A 697 MET cc_start: -0.4843 (ptp) cc_final: -0.5699 (ptt) outliers start: 44 outliers final: 31 residues processed: 233 average time/residue: 0.2171 time to fit residues: 68.3173 Evaluate side-chains 233 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 124 LYS Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 142 TYR Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 596 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 74 optimal weight: 4.9990 chunk 22 optimal weight: 0.0270 chunk 53 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 171 HIS L 168 GLN A 188 ASN A 448 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.214308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.180806 restraints weight = 18231.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.186160 restraints weight = 9750.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.189593 restraints weight = 5921.504| |-----------------------------------------------------------------------------| r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5856 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 8588 Z= 0.196 Angle : 0.570 9.621 11689 Z= 0.286 Chirality : 0.044 0.153 1302 Planarity : 0.004 0.055 1507 Dihedral : 6.929 87.967 1205 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 5.43 % Allowed : 16.29 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.76 (0.24), residues: 1065 helix: -1.62 (0.82), residues: 32 sheet: -1.05 (0.30), residues: 317 loop : -2.36 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 150 HIS 0.002 0.001 HIS L 191 PHE 0.015 0.001 PHE A 377 TYR 0.014 0.001 TYR A 265 ARG 0.004 0.000 ARG L 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 204 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.7820 (mp) cc_final: 0.6923 (tt) REVERT: H 52 ASN cc_start: 0.8298 (t0) cc_final: 0.8048 (t0) REVERT: H 85 SER cc_start: 0.7471 (t) cc_final: 0.7014 (p) REVERT: H 117 LEU cc_start: 0.8239 (tp) cc_final: 0.8008 (tp) REVERT: H 176 VAL cc_start: 0.7839 (t) cc_final: 0.7433 (p) REVERT: H 189 VAL cc_start: 0.8581 (t) cc_final: 0.8221 (p) REVERT: H 200 THR cc_start: 0.8566 (m) cc_final: 0.8230 (t) REVERT: H 201 TYR cc_start: 0.6339 (m-80) cc_final: 0.6061 (m-80) REVERT: L 46 LEU cc_start: 0.8176 (tp) cc_final: 0.7949 (tp) REVERT: L 83 PHE cc_start: 0.7477 (m-80) cc_final: 0.7099 (m-80) REVERT: L 97 MET cc_start: 0.6300 (mtm) cc_final: 0.5960 (mtm) REVERT: L 164 SER cc_start: 0.8429 (t) cc_final: 0.8118 (p) REVERT: L 168 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7425 (mt0) REVERT: L 178 SER cc_start: 0.8345 (t) cc_final: 0.7521 (m) REVERT: A 59 PHE cc_start: 0.7055 (m-10) cc_final: 0.6763 (m-10) REVERT: A 269 TYR cc_start: 0.7565 (m-80) cc_final: 0.7302 (m-80) REVERT: A 298 GLU cc_start: 0.7346 (tt0) cc_final: 0.7086 (tt0) REVERT: A 345 THR cc_start: 0.7180 (p) cc_final: 0.6903 (t) REVERT: A 357 ARG cc_start: 0.7624 (ptm-80) cc_final: 0.7105 (ptm-80) REVERT: A 378 LYS cc_start: 0.8147 (ptpp) cc_final: 0.7788 (ptpp) REVERT: A 382 VAL cc_start: 0.6062 (OUTLIER) cc_final: 0.5168 (p) REVERT: A 394 ASN cc_start: 0.6755 (t0) cc_final: 0.5950 (t0) REVERT: A 406 GLU cc_start: 0.7487 (pt0) cc_final: 0.7205 (pt0) REVERT: A 424 LYS cc_start: 0.7832 (ttmm) cc_final: 0.7548 (ttmm) REVERT: A 436 TRP cc_start: 0.7398 (p90) cc_final: 0.6818 (p90) REVERT: A 448 ASN cc_start: 0.7113 (m-40) cc_final: 0.6765 (m-40) REVERT: A 460 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7730 (mptm) REVERT: A 465 GLU cc_start: 0.6928 (tt0) cc_final: 0.6294 (tt0) REVERT: A 539 VAL cc_start: 0.7795 (t) cc_final: 0.7554 (p) REVERT: A 542 ASN cc_start: 0.6894 (t0) cc_final: 0.6675 (t0) REVERT: A 592 PHE cc_start: 0.1331 (OUTLIER) cc_final: -0.0552 (m-10) REVERT: A 697 MET cc_start: -0.4625 (ptp) cc_final: -0.5517 (ptt) outliers start: 51 outliers final: 34 residues processed: 237 average time/residue: 0.2248 time to fit residues: 71.2379 Evaluate side-chains 240 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 124 LYS Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 142 TYR Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain L residue 168 GLN Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 596 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 29 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 171 HIS L 90 HIS L 149 GLN A 422 ASN A 474 GLN A 677 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.205039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.171467 restraints weight = 17620.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.176815 restraints weight = 9537.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.180185 restraints weight = 5901.148| |-----------------------------------------------------------------------------| r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.143 8588 Z= 0.424 Angle : 0.759 10.755 11689 Z= 0.398 Chirality : 0.050 0.244 1302 Planarity : 0.005 0.061 1507 Dihedral : 7.930 87.608 1204 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer: Outliers : 6.07 % Allowed : 16.08 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.01 (0.24), residues: 1065 helix: -2.08 (0.75), residues: 31 sheet: -1.18 (0.30), residues: 300 loop : -2.53 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP L 35 HIS 0.007 0.002 HIS A 245 PHE 0.026 0.003 PHE A 377 TYR 0.031 0.002 TYR L 175 ARG 0.006 0.001 ARG L 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 215 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.7823 (mp) cc_final: 0.7313 (tt) REVERT: H 6 GLN cc_start: 0.7182 (tt0) cc_final: 0.6840 (tt0) REVERT: H 65 GLN cc_start: 0.7267 (tt0) cc_final: 0.7049 (tt0) REVERT: H 85 SER cc_start: 0.7724 (t) cc_final: 0.7218 (p) REVERT: H 116 THR cc_start: 0.7742 (m) cc_final: 0.7461 (p) REVERT: H 117 LEU cc_start: 0.8355 (tp) cc_final: 0.8077 (tp) REVERT: H 176 VAL cc_start: 0.7954 (t) cc_final: 0.7568 (p) REVERT: H 187 SER cc_start: 0.8459 (t) cc_final: 0.8162 (p) REVERT: H 200 THR cc_start: 0.8726 (m) cc_final: 0.8408 (t) REVERT: L 4 LEU cc_start: 0.7696 (mt) cc_final: 0.7382 (tp) REVERT: L 11 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7613 (tp) REVERT: L 46 LEU cc_start: 0.8241 (tp) cc_final: 0.8034 (tp) REVERT: L 58 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8288 (tt) REVERT: L 97 MET cc_start: 0.6387 (mtm) cc_final: 0.6033 (mtm) REVERT: L 107 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6644 (mm-30) REVERT: L 164 SER cc_start: 0.8451 (t) cc_final: 0.8134 (p) REVERT: L 178 SER cc_start: 0.8377 (t) cc_final: 0.7580 (m) REVERT: A 59 PHE cc_start: 0.6821 (m-10) cc_final: 0.6498 (m-10) REVERT: A 126 ASN cc_start: 0.6124 (p0) cc_final: 0.5781 (p0) REVERT: A 239 GLN cc_start: 0.6500 (mm-40) cc_final: 0.6201 (mm-40) REVERT: A 298 GLU cc_start: 0.7494 (tt0) cc_final: 0.7022 (tt0) REVERT: A 345 THR cc_start: 0.7354 (p) cc_final: 0.7131 (t) REVERT: A 357 ARG cc_start: 0.7667 (ptm-80) cc_final: 0.7165 (ptm-80) REVERT: A 394 ASN cc_start: 0.6950 (t0) cc_final: 0.6213 (t0) REVERT: A 406 GLU cc_start: 0.7405 (pt0) cc_final: 0.7145 (pt0) REVERT: A 414 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7462 (mm110) REVERT: A 424 LYS cc_start: 0.8129 (ttmm) cc_final: 0.7840 (ttmm) REVERT: A 436 TRP cc_start: 0.7608 (p90) cc_final: 0.6923 (p90) REVERT: A 448 ASN cc_start: 0.7450 (m-40) cc_final: 0.7166 (m-40) REVERT: A 460 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7799 (mptm) REVERT: A 465 GLU cc_start: 0.6891 (tt0) cc_final: 0.6300 (tt0) REVERT: A 542 ASN cc_start: 0.6754 (t0) cc_final: 0.6515 (t0) REVERT: A 592 PHE cc_start: 0.3179 (OUTLIER) cc_final: -0.0197 (m-80) REVERT: A 697 MET cc_start: -0.3985 (ptp) cc_final: -0.5196 (ptt) outliers start: 57 outliers final: 37 residues processed: 246 average time/residue: 0.2166 time to fit residues: 72.5291 Evaluate side-chains 248 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 207 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain L residue 211 PHE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 677 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 57 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 17 optimal weight: 0.4980 chunk 94 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 171 HIS A 493 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.207342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.174269 restraints weight = 18090.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.179571 restraints weight = 9760.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.182895 restraints weight = 6003.999| |-----------------------------------------------------------------------------| r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6040 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 8588 Z= 0.268 Angle : 0.672 9.545 11689 Z= 0.346 Chirality : 0.048 0.258 1302 Planarity : 0.005 0.069 1507 Dihedral : 7.354 87.351 1197 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 4.90 % Allowed : 18.74 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.92 (0.24), residues: 1065 helix: -1.99 (0.79), residues: 31 sheet: -1.19 (0.29), residues: 305 loop : -2.43 (0.21), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 105 HIS 0.004 0.001 HIS A 245 PHE 0.025 0.002 PHE A 377 TYR 0.021 0.002 TYR A 265 ARG 0.006 0.000 ARG L 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 215 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.7828 (mp) cc_final: 0.7374 (tt) REVERT: H 6 GLN cc_start: 0.7106 (tt0) cc_final: 0.6767 (tt0) REVERT: H 65 GLN cc_start: 0.7250 (tt0) cc_final: 0.7041 (tt0) REVERT: H 85 SER cc_start: 0.7666 (t) cc_final: 0.7187 (p) REVERT: H 89 GLU cc_start: 0.8136 (pp20) cc_final: 0.7536 (pp20) REVERT: H 116 THR cc_start: 0.7617 (m) cc_final: 0.7355 (p) REVERT: H 117 LEU cc_start: 0.8327 (tp) cc_final: 0.8081 (tp) REVERT: H 176 VAL cc_start: 0.7923 (t) cc_final: 0.7539 (p) REVERT: H 187 SER cc_start: 0.8348 (t) cc_final: 0.8030 (p) REVERT: H 189 VAL cc_start: 0.8851 (t) cc_final: 0.8378 (p) REVERT: H 200 THR cc_start: 0.8707 (m) cc_final: 0.8415 (t) REVERT: L 4 LEU cc_start: 0.7518 (mt) cc_final: 0.7141 (tp) REVERT: L 14 SER cc_start: 0.8611 (m) cc_final: 0.8399 (t) REVERT: L 46 LEU cc_start: 0.8228 (tp) cc_final: 0.8013 (tp) REVERT: L 58 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8293 (tt) REVERT: L 83 PHE cc_start: 0.7528 (m-80) cc_final: 0.7174 (m-80) REVERT: L 97 MET cc_start: 0.6387 (mtm) cc_final: 0.6161 (mtm) REVERT: L 107 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6519 (mm-30) REVERT: L 164 SER cc_start: 0.8497 (t) cc_final: 0.8171 (p) REVERT: L 178 SER cc_start: 0.8321 (t) cc_final: 0.7555 (m) REVERT: A 59 PHE cc_start: 0.6846 (m-10) cc_final: 0.6379 (m-10) REVERT: A 60 PHE cc_start: 0.8132 (m-80) cc_final: 0.7775 (m-10) REVERT: A 126 ASN cc_start: 0.6111 (p0) cc_final: 0.5802 (p0) REVERT: A 298 GLU cc_start: 0.7396 (tt0) cc_final: 0.6910 (tt0) REVERT: A 331 ASN cc_start: 0.7189 (t0) cc_final: 0.6966 (t0) REVERT: A 357 ARG cc_start: 0.7699 (ptm-80) cc_final: 0.7404 (ptm-80) REVERT: A 378 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8094 (ptpp) REVERT: A 394 ASN cc_start: 0.6975 (t0) cc_final: 0.6600 (t0) REVERT: A 406 GLU cc_start: 0.7396 (pt0) cc_final: 0.6151 (pt0) REVERT: A 409 GLN cc_start: 0.7788 (mt0) cc_final: 0.7471 (mt0) REVERT: A 424 LYS cc_start: 0.8039 (ttmm) cc_final: 0.7741 (ttmm) REVERT: A 448 ASN cc_start: 0.7206 (m-40) cc_final: 0.6954 (m-40) REVERT: A 460 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7811 (mptm) REVERT: A 465 GLU cc_start: 0.6866 (tt0) cc_final: 0.6311 (tt0) REVERT: A 515 PHE cc_start: 0.7637 (m-10) cc_final: 0.7376 (m-10) REVERT: A 542 ASN cc_start: 0.7018 (t0) cc_final: 0.6818 (t0) REVERT: A 592 PHE cc_start: 0.2791 (OUTLIER) cc_final: -0.0541 (m-80) outliers start: 46 outliers final: 36 residues processed: 235 average time/residue: 0.2213 time to fit residues: 69.6244 Evaluate side-chains 248 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain L residue 211 PHE Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 596 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 19 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 171 HIS L 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.208259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.174987 restraints weight = 17896.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.180330 restraints weight = 9649.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.183753 restraints weight = 5934.829| |-----------------------------------------------------------------------------| r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6013 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8588 Z= 0.214 Angle : 0.645 8.562 11689 Z= 0.329 Chirality : 0.046 0.206 1302 Planarity : 0.005 0.067 1507 Dihedral : 7.263 87.204 1196 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 4.69 % Allowed : 18.96 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.83 (0.24), residues: 1065 helix: -2.21 (0.76), residues: 32 sheet: -1.18 (0.29), residues: 313 loop : -2.33 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 105 HIS 0.003 0.001 HIS A 67 PHE 0.019 0.002 PHE A 377 TYR 0.016 0.001 TYR A 265 ARG 0.007 0.000 ARG L 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.7850 (mp) cc_final: 0.7396 (tt) REVERT: H 6 GLN cc_start: 0.7095 (tt0) cc_final: 0.6749 (tt0) REVERT: H 85 SER cc_start: 0.7595 (t) cc_final: 0.7121 (p) REVERT: H 116 THR cc_start: 0.7612 (m) cc_final: 0.7340 (p) REVERT: H 117 LEU cc_start: 0.8309 (tp) cc_final: 0.8067 (tp) REVERT: H 124 LYS cc_start: 0.5942 (OUTLIER) cc_final: 0.5721 (mtpm) REVERT: H 176 VAL cc_start: 0.7888 (t) cc_final: 0.7505 (p) REVERT: H 187 SER cc_start: 0.8288 (t) cc_final: 0.7961 (p) REVERT: H 189 VAL cc_start: 0.8789 (t) cc_final: 0.8346 (p) REVERT: H 200 THR cc_start: 0.8707 (m) cc_final: 0.8460 (t) REVERT: L 4 LEU cc_start: 0.7557 (mt) cc_final: 0.7251 (tp) REVERT: L 83 PHE cc_start: 0.7498 (m-80) cc_final: 0.7152 (m-80) REVERT: L 107 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6475 (mm-30) REVERT: L 164 SER cc_start: 0.8515 (t) cc_final: 0.8189 (p) REVERT: L 174 THR cc_start: 0.8351 (p) cc_final: 0.8020 (t) REVERT: L 178 SER cc_start: 0.8300 (t) cc_final: 0.7558 (m) REVERT: A 59 PHE cc_start: 0.6852 (m-10) cc_final: 0.6385 (m-10) REVERT: A 60 PHE cc_start: 0.8076 (m-80) cc_final: 0.7720 (m-10) REVERT: A 126 ASN cc_start: 0.6112 (p0) cc_final: 0.5814 (p0) REVERT: A 298 GLU cc_start: 0.7386 (tt0) cc_final: 0.6878 (tt0) REVERT: A 331 ASN cc_start: 0.7122 (t0) cc_final: 0.6899 (t0) REVERT: A 357 ARG cc_start: 0.7667 (ptm-80) cc_final: 0.7195 (ptm-80) REVERT: A 394 ASN cc_start: 0.6908 (t0) cc_final: 0.6380 (t0) REVERT: A 406 GLU cc_start: 0.7398 (pt0) cc_final: 0.7135 (pt0) REVERT: A 424 LYS cc_start: 0.8012 (ttmm) cc_final: 0.7708 (ttmm) REVERT: A 425 LEU cc_start: 0.8373 (mm) cc_final: 0.7841 (mt) REVERT: A 448 ASN cc_start: 0.7219 (m-40) cc_final: 0.6967 (m-40) REVERT: A 460 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7765 (mptm) REVERT: A 465 GLU cc_start: 0.6871 (tt0) cc_final: 0.6310 (tt0) REVERT: A 515 PHE cc_start: 0.7639 (m-10) cc_final: 0.7412 (m-10) REVERT: A 542 ASN cc_start: 0.7139 (t0) cc_final: 0.6931 (t0) REVERT: A 592 PHE cc_start: 0.2932 (OUTLIER) cc_final: -0.0647 (m-10) outliers start: 44 outliers final: 38 residues processed: 230 average time/residue: 0.2169 time to fit residues: 68.3144 Evaluate side-chains 246 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 205 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 124 LYS Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain L residue 211 PHE Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 596 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 98 optimal weight: 0.3980 chunk 45 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 80 optimal weight: 0.0270 chunk 68 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 15 optimal weight: 0.0050 chunk 7 optimal weight: 3.9990 chunk 73 optimal weight: 0.0770 chunk 60 optimal weight: 0.0670 overall best weight: 0.1148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 171 HIS A 422 ASN A 474 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.212791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.180628 restraints weight = 18560.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.185716 restraints weight = 10018.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.188993 restraints weight = 6170.352| |-----------------------------------------------------------------------------| r_work (final): 0.4331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5904 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8588 Z= 0.166 Angle : 0.629 9.108 11689 Z= 0.317 Chirality : 0.046 0.221 1302 Planarity : 0.004 0.064 1507 Dihedral : 7.033 86.926 1196 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 4.37 % Allowed : 19.70 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.54 (0.25), residues: 1065 helix: -1.69 (0.81), residues: 32 sheet: -0.83 (0.30), residues: 301 loop : -2.21 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 35 HIS 0.001 0.000 HIS H 171 PHE 0.018 0.001 PHE L 118 TYR 0.011 0.001 TYR L 194 ARG 0.006 0.000 ARG L 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 206 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.7797 (mp) cc_final: 0.7475 (tt) REVERT: H 6 GLN cc_start: 0.6993 (tt0) cc_final: 0.6628 (tt0) REVERT: H 85 SER cc_start: 0.7380 (t) cc_final: 0.6953 (p) REVERT: H 116 THR cc_start: 0.7514 (m) cc_final: 0.7245 (p) REVERT: H 117 LEU cc_start: 0.8263 (tp) cc_final: 0.8036 (tp) REVERT: H 172 THR cc_start: 0.8337 (m) cc_final: 0.7756 (p) REVERT: H 176 VAL cc_start: 0.7860 (t) cc_final: 0.7481 (p) REVERT: H 200 THR cc_start: 0.8708 (m) cc_final: 0.8418 (t) REVERT: H 201 TYR cc_start: 0.6084 (m-80) cc_final: 0.5872 (m-80) REVERT: L 4 LEU cc_start: 0.7393 (mt) cc_final: 0.6907 (tp) REVERT: L 14 SER cc_start: 0.8458 (m) cc_final: 0.8244 (t) REVERT: L 58 ILE cc_start: 0.8650 (mm) cc_final: 0.8159 (tt) REVERT: L 83 PHE cc_start: 0.7355 (m-80) cc_final: 0.7124 (m-80) REVERT: L 107 GLU cc_start: 0.6759 (mm-30) cc_final: 0.6377 (mm-30) REVERT: L 164 SER cc_start: 0.8594 (t) cc_final: 0.8259 (p) REVERT: L 178 SER cc_start: 0.8270 (t) cc_final: 0.7563 (m) REVERT: A 59 PHE cc_start: 0.6884 (m-10) cc_final: 0.6596 (m-10) REVERT: A 60 PHE cc_start: 0.7898 (m-80) cc_final: 0.7559 (m-10) REVERT: A 298 GLU cc_start: 0.7255 (tt0) cc_final: 0.6848 (tt0) REVERT: A 320 VAL cc_start: 0.5307 (m) cc_final: 0.4910 (t) REVERT: A 353 TRP cc_start: 0.8026 (p-90) cc_final: 0.7632 (p-90) REVERT: A 357 ARG cc_start: 0.7698 (ptm-80) cc_final: 0.7229 (ptm-80) REVERT: A 378 LYS cc_start: 0.8088 (pttm) cc_final: 0.7738 (ptpp) REVERT: A 380 TYR cc_start: 0.6156 (m-80) cc_final: 0.5766 (m-80) REVERT: A 394 ASN cc_start: 0.6863 (t0) cc_final: 0.6379 (t0) REVERT: A 406 GLU cc_start: 0.7436 (pt0) cc_final: 0.7181 (pt0) REVERT: A 424 LYS cc_start: 0.7819 (ttmm) cc_final: 0.7494 (ttmm) REVERT: A 448 ASN cc_start: 0.7023 (m-40) cc_final: 0.6730 (m-40) REVERT: A 458 LYS cc_start: 0.8860 (ttmt) cc_final: 0.8575 (ttmm) REVERT: A 460 LYS cc_start: 0.8180 (mptm) cc_final: 0.7689 (mptm) REVERT: A 465 GLU cc_start: 0.6881 (tt0) cc_final: 0.6424 (tt0) REVERT: A 592 PHE cc_start: 0.2490 (OUTLIER) cc_final: -0.0507 (m-10) outliers start: 41 outliers final: 35 residues processed: 229 average time/residue: 0.2245 time to fit residues: 69.0287 Evaluate side-chains 236 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain L residue 211 PHE Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 596 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 20 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 96 optimal weight: 20.0000 chunk 52 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN H 65 GLN H 171 HIS A 31 ASN A 422 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.207262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.173185 restraints weight = 18047.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.178626 restraints weight = 9881.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.182077 restraints weight = 6156.916| |-----------------------------------------------------------------------------| r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6090 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8588 Z= 0.305 Angle : 0.696 9.387 11689 Z= 0.359 Chirality : 0.048 0.262 1302 Planarity : 0.005 0.072 1507 Dihedral : 7.395 86.985 1196 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.17 % Favored : 88.83 % Rotamer: Outliers : 4.15 % Allowed : 19.81 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.74 (0.25), residues: 1065 helix: -1.96 (0.78), residues: 31 sheet: -1.11 (0.30), residues: 321 loop : -2.29 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP L 150 HIS 0.006 0.001 HIS L 191 PHE 0.035 0.002 PHE A 377 TYR 0.020 0.002 TYR L 142 ARG 0.011 0.001 ARG L 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 211 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.7913 (mp) cc_final: 0.7431 (tt) REVERT: H 6 GLN cc_start: 0.7151 (tt0) cc_final: 0.6810 (tt0) REVERT: H 85 SER cc_start: 0.7498 (t) cc_final: 0.7033 (p) REVERT: H 116 THR cc_start: 0.7653 (m) cc_final: 0.7387 (p) REVERT: H 117 LEU cc_start: 0.8345 (tp) cc_final: 0.8123 (tp) REVERT: H 172 THR cc_start: 0.8400 (m) cc_final: 0.7852 (p) REVERT: H 176 VAL cc_start: 0.7949 (t) cc_final: 0.7575 (p) REVERT: H 187 SER cc_start: 0.8332 (t) cc_final: 0.8026 (p) REVERT: H 189 VAL cc_start: 0.8822 (t) cc_final: 0.8338 (p) REVERT: H 200 THR cc_start: 0.8750 (m) cc_final: 0.8504 (t) REVERT: L 4 LEU cc_start: 0.7622 (mt) cc_final: 0.7335 (tp) REVERT: L 14 SER cc_start: 0.8573 (m) cc_final: 0.8273 (t) REVERT: L 58 ILE cc_start: 0.8745 (mm) cc_final: 0.8270 (tt) REVERT: L 83 PHE cc_start: 0.7512 (m-80) cc_final: 0.7205 (m-80) REVERT: L 107 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6656 (mm-30) REVERT: L 164 SER cc_start: 0.8470 (t) cc_final: 0.8153 (p) REVERT: L 178 SER cc_start: 0.8382 (t) cc_final: 0.7612 (m) REVERT: A 59 PHE cc_start: 0.6945 (m-10) cc_final: 0.6511 (m-10) REVERT: A 60 PHE cc_start: 0.8233 (m-80) cc_final: 0.7824 (m-10) REVERT: A 126 ASN cc_start: 0.6046 (p0) cc_final: 0.5743 (p0) REVERT: A 298 GLU cc_start: 0.7516 (tt0) cc_final: 0.7022 (tt0) REVERT: A 353 TRP cc_start: 0.8196 (p-90) cc_final: 0.7554 (p-90) REVERT: A 357 ARG cc_start: 0.7647 (ptm-80) cc_final: 0.7390 (ptm-80) REVERT: A 380 TYR cc_start: 0.6342 (m-80) cc_final: 0.5796 (m-80) REVERT: A 394 ASN cc_start: 0.7002 (t0) cc_final: 0.6737 (t0) REVERT: A 406 GLU cc_start: 0.7396 (pt0) cc_final: 0.7135 (pt0) REVERT: A 424 LYS cc_start: 0.8092 (ttmm) cc_final: 0.7782 (ttmm) REVERT: A 433 VAL cc_start: 0.7977 (p) cc_final: 0.7701 (p) REVERT: A 448 ASN cc_start: 0.7469 (m-40) cc_final: 0.7134 (m-40) REVERT: A 460 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7784 (mptm) REVERT: A 465 GLU cc_start: 0.6882 (tt0) cc_final: 0.6385 (tt0) REVERT: A 592 PHE cc_start: 0.3260 (OUTLIER) cc_final: -0.0422 (m-10) outliers start: 39 outliers final: 34 residues processed: 230 average time/residue: 0.2038 time to fit residues: 64.7324 Evaluate side-chains 246 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 210 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain L residue 211 PHE Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 596 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 64 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 101 optimal weight: 0.2980 chunk 92 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 0.0980 chunk 21 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 65 optimal weight: 0.1980 overall best weight: 0.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN H 171 HIS L 102 GLN A 70 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.210126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.177024 restraints weight = 18201.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.182517 restraints weight = 9637.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.185970 restraints weight = 5857.158| |-----------------------------------------------------------------------------| r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5973 moved from start: 0.5353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8588 Z= 0.174 Angle : 0.632 8.800 11689 Z= 0.318 Chirality : 0.046 0.170 1302 Planarity : 0.005 0.069 1507 Dihedral : 7.120 86.630 1196 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 3.94 % Allowed : 20.13 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.50 (0.25), residues: 1065 helix: -1.82 (0.79), residues: 32 sheet: -0.88 (0.30), residues: 314 loop : -2.14 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 105 HIS 0.002 0.000 HIS A 67 PHE 0.019 0.002 PHE L 118 TYR 0.016 0.001 TYR A 453 ARG 0.008 0.000 ARG L 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3238.15 seconds wall clock time: 58 minutes 41.05 seconds (3521.05 seconds total)