Starting phenix.real_space_refine on Tue Apr 29 05:34:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kej_37160/04_2025/8kej_37160.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kej_37160/04_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_37160/04_2025/8kej_37160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kej_37160/04_2025/8kej_37160.map" model { file = "/net/cci-nas-00/data/ceres_data/8kej_37160/04_2025/8kej_37160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kej_37160/04_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-5669/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: 5.60, per 1000 atoms: 0.67 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: 2.15 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.09 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: 2.62 Time building geometry restraints manager: 2.58 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.630 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.480 ------------------------------------------------------------------------------- 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 8600 Z= 0.195 Angle : 0.653 6.219 11713 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 Details of bonding type rmsd hydrogen bonds : bond 0.28674 ( 180) hydrogen bonds : angle 11.18339 ( 471) SS BOND : bond 0.00125 ( 12) SS BOND : angle 0.34960 ( 24) covalent geometry : bond 0.00295 ( 8588) covalent geometry : angle 0.65302 (11689) *********************** 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 : 0.840 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: 0.2151 time to fit residues: 76.4447 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 : 0.902 ------------------------------------------------------------------------------- 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 = 0.218451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.184228 restraints weight = 18342.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.189668 restraints weight = 9623.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.193102 restraints weight = 5759.254| |-----------------------------------------------------------------------------| r_work (final): 0.4377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5755 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 8600 Z= 0.147 Angle : 0.609 10.588 11713 Z= 0.312 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 Details of bonding type rmsd hydrogen bonds : bond 0.04536 ( 180) hydrogen bonds : angle 7.73284 ( 471) SS BOND : bond 0.00492 ( 12) SS BOND : angle 1.24462 ( 24) covalent geometry : bond 0.00339 ( 8588) covalent geometry : angle 0.60660 (11689) *********************** 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 : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.7771 (mp) cc_final: 0.7025 (tt) REVERT: H 29 PHE cc_start: 0.8009 (t80) cc_final: 0.7809 (t80) REVERT: H 68 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8050 (t) REVERT: H 85 SER cc_start: 0.7733 (t) cc_final: 0.7297 (p) REVERT: H 103 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.6142 (mt) REVERT: H 117 LEU cc_start: 0.8204 (tp) cc_final: 0.7989 (tp) REVERT: H 148 LEU cc_start: 0.8092 (tt) cc_final: 0.7861 (tt) REVERT: H 160 SER cc_start: 0.8012 (p) cc_final: 0.7722 (t) REVERT: H 176 VAL cc_start: 0.7688 (t) cc_final: 0.7251 (p) REVERT: H 189 VAL cc_start: 0.8654 (t) cc_final: 0.8263 (p) REVERT: H 200 THR cc_start: 0.8520 (m) cc_final: 0.8174 (t) REVERT: H 201 TYR cc_start: 0.6457 (m-80) cc_final: 0.6159 (m-80) REVERT: L 11 LEU cc_start: 0.7596 (tp) cc_final: 0.7357 (mm) REVERT: L 14 SER cc_start: 0.8129 (t) cc_final: 0.7913 (m) REVERT: L 46 LEU cc_start: 0.8046 (tp) cc_final: 0.7728 (tp) REVERT: L 82 ASP cc_start: 0.8199 (m-30) cc_final: 0.7988 (m-30) REVERT: L 83 PHE cc_start: 0.7538 (m-80) cc_final: 0.7148 (m-80) REVERT: L 97 MET cc_start: 0.6242 (mtm) cc_final: 0.5729 (mtm) REVERT: L 164 SER cc_start: 0.8397 (t) cc_final: 0.7980 (p) REVERT: L 171 LYS cc_start: 0.8481 (mttt) cc_final: 0.8264 (mttt) REVERT: L 178 SER cc_start: 0.8296 (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: 0.7175 (m-10) cc_final: 0.6972 (m-10) REVERT: A 147 LYS cc_start: 0.4537 (mmmt) cc_final: 0.4328 (mmmt) REVERT: A 269 TYR cc_start: 0.7556 (m-80) cc_final: 0.7318 (m-80) REVERT: A 298 GLU cc_start: 0.7283 (tt0) cc_final: 0.7081 (tt0) REVERT: A 310 LYS cc_start: 0.7363 (mtmt) cc_final: 0.6831 (ptpp) REVERT: A 357 ARG cc_start: 0.7536 (ptm-80) cc_final: 0.7273 (ptm-80) REVERT: A 378 LYS cc_start: 0.8039 (ptpp) cc_final: 0.7577 (pttm) REVERT: A 382 VAL cc_start: 0.5915 (OUTLIER) cc_final: 0.4987 (p) REVERT: A 436 TRP cc_start: 0.7232 (p90) cc_final: 0.6792 (p90) REVERT: A 448 ASN cc_start: 0.6989 (m110) cc_final: 0.6617 (m-40) REVERT: A 460 LYS cc_start: 0.8164 (mptm) cc_final: 0.7713 (mptm) REVERT: A 510 VAL cc_start: 0.8178 (t) cc_final: 0.7942 (m) REVERT: A 542 ASN cc_start: 0.6933 (t0) cc_final: 0.6695 (t0) REVERT: A 592 PHE cc_start: 0.1046 (OUTLIER) cc_final: -0.0479 (m-10) REVERT: A 697 MET cc_start: -0.4684 (ptp) cc_final: -0.5686 (ptt) outliers start: 44 outliers final: 27 residues processed: 251 average time/residue: 0.2142 time to fit residues: 72.5781 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 : 0.828 ------------------------------------------------------------------------------- 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: 1.9990 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 98 optimal weight: 0.2980 chunk 94 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.216533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.182704 restraints weight = 18520.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.187949 restraints weight = 9977.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.191268 restraints weight = 6076.168| |-----------------------------------------------------------------------------| r_work (final): 0.4361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5820 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8600 Z= 0.131 Angle : 0.581 10.078 11713 Z= 0.299 Chirality : 0.045 0.178 1302 Planarity : 0.004 0.052 1507 Dihedral : 6.965 87.858 1206 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 4.58 % Allowed : 14.70 % 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: -3.23 (0.23), residues: 1065 helix: -1.84 (0.77), residues: 26 sheet: -1.46 (0.28), residues: 338 loop : -2.66 (0.21), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP L 150 HIS 0.002 0.001 HIS H 207 PHE 0.019 0.002 PHE H 129 TYR 0.015 0.001 TYR A 265 ARG 0.004 0.000 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.03591 ( 180) hydrogen bonds : angle 7.00811 ( 471) SS BOND : bond 0.00396 ( 12) SS BOND : angle 1.18640 ( 24) covalent geometry : bond 0.00303 ( 8588) covalent geometry : angle 0.57873 (11689) *********************** 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: 43 poor density : 201 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.7807 (mp) cc_final: 0.7006 (tt) REVERT: H 29 PHE cc_start: 0.8041 (t80) cc_final: 0.7799 (t80) REVERT: H 34 MET cc_start: 0.7130 (mmm) cc_final: 0.6794 (mmm) REVERT: H 36 TRP cc_start: 0.7177 (t-100) cc_final: 0.6686 (m-90) REVERT: H 85 SER cc_start: 0.7707 (t) cc_final: 0.7233 (p) REVERT: H 148 LEU cc_start: 0.8044 (tt) cc_final: 0.7825 (tt) REVERT: H 160 SER cc_start: 0.7996 (p) cc_final: 0.7737 (t) REVERT: H 172 THR cc_start: 0.8461 (m) cc_final: 0.7899 (p) REVERT: H 176 VAL cc_start: 0.7848 (t) cc_final: 0.7431 (p) REVERT: H 189 VAL cc_start: 0.8604 (t) cc_final: 0.8234 (p) REVERT: H 200 THR cc_start: 0.8529 (m) cc_final: 0.8175 (t) REVERT: H 201 TYR cc_start: 0.6420 (m-80) cc_final: 0.6143 (m-80) REVERT: L 14 SER cc_start: 0.8231 (t) cc_final: 0.8029 (m) REVERT: L 46 LEU cc_start: 0.8127 (tp) cc_final: 0.7830 (tp) REVERT: L 83 PHE cc_start: 0.7553 (m-80) cc_final: 0.7184 (m-80) REVERT: L 97 MET cc_start: 0.6257 (mtm) cc_final: 0.5857 (mtm) REVERT: L 164 SER cc_start: 0.8393 (t) cc_final: 0.8061 (p) REVERT: L 178 SER cc_start: 0.8294 (t) cc_final: 0.7375 (m) REVERT: A 57 LEU cc_start: 0.7486 (tp) cc_final: 0.7098 (tp) REVERT: A 59 PHE cc_start: 0.7150 (m-10) cc_final: 0.6915 (m-10) REVERT: A 269 TYR cc_start: 0.7633 (m-80) cc_final: 0.7379 (m-80) REVERT: A 298 GLU cc_start: 0.7370 (tt0) cc_final: 0.7119 (tt0) REVERT: A 310 LYS cc_start: 0.7484 (mtmt) cc_final: 0.7221 (mtpt) REVERT: A 357 ARG cc_start: 0.7631 (ptm-80) cc_final: 0.7208 (ptm-80) REVERT: A 369 TYR cc_start: 0.7228 (m-80) cc_final: 0.7021 (m-10) REVERT: A 378 LYS cc_start: 0.8117 (ptpp) cc_final: 0.7773 (ptpp) REVERT: A 382 VAL cc_start: 0.5980 (OUTLIER) cc_final: 0.5044 (p) REVERT: A 394 ASN cc_start: 0.6344 (t0) cc_final: 0.5778 (t0) REVERT: A 406 GLU cc_start: 0.7503 (pt0) cc_final: 0.7193 (pt0) REVERT: A 424 LYS cc_start: 0.8020 (ttmm) cc_final: 0.7778 (ttmm) REVERT: A 436 TRP cc_start: 0.7282 (p90) cc_final: 0.6810 (p90) REVERT: A 438 SER cc_start: 0.8179 (p) cc_final: 0.7823 (t) REVERT: A 448 ASN cc_start: 0.7072 (m110) cc_final: 0.6714 (m-40) REVERT: A 460 LYS cc_start: 0.8240 (mptm) cc_final: 0.7779 (mptm) REVERT: A 465 GLU cc_start: 0.6939 (tt0) cc_final: 0.6386 (tt0) REVERT: A 510 VAL cc_start: 0.8197 (t) cc_final: 0.7970 (m) REVERT: A 542 ASN cc_start: 0.6934 (t0) cc_final: 0.6684 (t0) REVERT: A 592 PHE cc_start: 0.1286 (OUTLIER) cc_final: -0.0537 (m-80) REVERT: A 697 MET cc_start: -0.4754 (ptp) cc_final: -0.5714 (ptt) outliers start: 43 outliers final: 32 residues processed: 230 average time/residue: 0.2154 time to fit residues: 66.6433 Evaluate side-chains 230 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 40 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 4 optimal weight: 0.4980 chunk 89 optimal weight: 0.9990 chunk 103 optimal weight: 0.0980 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 171 HIS L 149 GLN A 188 ASN A 207 HIS A 314 GLN A 448 ASN A 474 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.213170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.179222 restraints weight = 18165.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.184634 restraints weight = 9766.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.188076 restraints weight = 5957.023| |-----------------------------------------------------------------------------| r_work (final): 0.4310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5884 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8600 Z= 0.143 Angle : 0.585 9.102 11713 Z= 0.300 Chirality : 0.045 0.185 1302 Planarity : 0.004 0.056 1507 Dihedral : 7.102 87.755 1205 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 5.11 % Allowed : 15.34 % Favored : 79.55 % 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: -3.03 (0.24), residues: 1065 helix: -2.01 (0.76), residues: 32 sheet: -1.27 (0.29), residues: 319 loop : -2.52 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 150 HIS 0.005 0.001 HIS L 191 PHE 0.023 0.002 PHE A 374 TYR 0.017 0.001 TYR A 265 ARG 0.005 0.000 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.03220 ( 180) hydrogen bonds : angle 6.51251 ( 471) SS BOND : bond 0.00443 ( 12) SS BOND : angle 1.31190 ( 24) covalent geometry : bond 0.00321 ( 8588) covalent geometry : angle 0.58274 (11689) *********************** 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 260 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 212 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.7759 (mp) cc_final: 0.6663 (tt) REVERT: H 34 MET cc_start: 0.7289 (mmm) cc_final: 0.6982 (mmm) REVERT: H 36 TRP cc_start: 0.7225 (t-100) cc_final: 0.6670 (m-90) REVERT: H 52 ASN cc_start: 0.8319 (t0) cc_final: 0.8108 (t0) REVERT: H 60 TYR cc_start: 0.8924 (m-80) cc_final: 0.8721 (m-80) REVERT: H 68 VAL cc_start: 0.8550 (OUTLIER) cc_final: 0.8293 (t) REVERT: H 85 SER cc_start: 0.7626 (t) cc_final: 0.7152 (p) REVERT: H 96 CYS cc_start: 0.5136 (p) cc_final: 0.3358 (p) REVERT: H 116 THR cc_start: 0.7642 (m) cc_final: 0.7252 (p) REVERT: H 117 LEU cc_start: 0.8262 (tp) cc_final: 0.7948 (tp) REVERT: H 172 THR cc_start: 0.8466 (m) cc_final: 0.7901 (p) REVERT: H 176 VAL cc_start: 0.7868 (t) cc_final: 0.7467 (p) REVERT: H 189 VAL cc_start: 0.8709 (t) cc_final: 0.8304 (p) REVERT: H 200 THR cc_start: 0.8575 (m) cc_final: 0.8221 (t) REVERT: H 201 TYR cc_start: 0.6374 (m-80) cc_final: 0.6084 (m-80) REVERT: L 46 LEU cc_start: 0.8206 (tp) cc_final: 0.7957 (tp) REVERT: L 83 PHE cc_start: 0.7526 (m-80) cc_final: 0.7128 (m-80) REVERT: L 97 MET cc_start: 0.6361 (mtm) cc_final: 0.5881 (mtm) REVERT: L 164 SER cc_start: 0.8421 (t) cc_final: 0.8114 (p) REVERT: L 168 GLN cc_start: 0.7962 (tt0) cc_final: 0.7437 (mt0) REVERT: L 178 SER cc_start: 0.8383 (t) cc_final: 0.7505 (m) REVERT: L 188 TYR cc_start: 0.7266 (t80) cc_final: 0.7048 (t80) REVERT: A 59 PHE cc_start: 0.7054 (m-10) cc_final: 0.6804 (m-10) REVERT: A 269 TYR cc_start: 0.7552 (m-80) cc_final: 0.7319 (m-80) REVERT: A 298 GLU cc_start: 0.7410 (tt0) cc_final: 0.7122 (tt0) REVERT: A 345 THR cc_start: 0.7161 (p) cc_final: 0.6894 (t) REVERT: A 353 TRP cc_start: 0.8127 (p-90) cc_final: 0.7609 (p-90) REVERT: A 357 ARG cc_start: 0.7639 (ptm-80) cc_final: 0.7261 (ptm-80) REVERT: A 369 TYR cc_start: 0.7377 (m-80) cc_final: 0.7157 (m-10) REVERT: A 378 LYS cc_start: 0.8134 (ptpp) cc_final: 0.7820 (ptpp) REVERT: A 382 VAL cc_start: 0.6111 (OUTLIER) cc_final: 0.5213 (p) REVERT: A 406 GLU cc_start: 0.7418 (pt0) cc_final: 0.7195 (pt0) REVERT: A 424 LYS cc_start: 0.8018 (ttmm) cc_final: 0.7737 (ttmm) REVERT: A 436 TRP cc_start: 0.7353 (p90) cc_final: 0.6818 (p90) REVERT: A 448 ASN cc_start: 0.7173 (m-40) cc_final: 0.6822 (m-40) REVERT: A 460 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7785 (mptm) REVERT: A 465 GLU cc_start: 0.6998 (tt0) cc_final: 0.6393 (tt0) REVERT: A 510 VAL cc_start: 0.8197 (t) cc_final: 0.7933 (m) REVERT: A 542 ASN cc_start: 0.6784 (t0) cc_final: 0.6551 (t0) REVERT: A 592 PHE cc_start: 0.1554 (OUTLIER) cc_final: -0.0423 (m-10) REVERT: A 697 MET cc_start: -0.4555 (ptp) cc_final: -0.5489 (ptt) outliers start: 48 outliers final: 31 residues processed: 242 average time/residue: 0.2062 time to fit residues: 67.8596 Evaluate side-chains 242 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 207 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 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 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 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 450 ASN Chi-restraints excluded: chain A residue 460 LYS 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: 1.9990 chunk 22 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 66 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 71 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 171 HIS L 126 GLN A 474 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.214486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.180842 restraints weight = 18201.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.186191 restraints weight = 9733.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.189634 restraints weight = 5891.221| |-----------------------------------------------------------------------------| r_work (final): 0.4330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5850 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 8600 Z= 0.106 Angle : 0.570 8.631 11713 Z= 0.285 Chirality : 0.044 0.148 1302 Planarity : 0.004 0.057 1507 Dihedral : 6.823 87.738 1201 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 5.22 % Allowed : 16.29 % Favored : 78.49 % 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: -2.75 (0.25), residues: 1065 helix: -1.58 (0.84), residues: 32 sheet: -1.06 (0.30), residues: 315 loop : -2.34 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 150 HIS 0.002 0.000 HIS L 90 PHE 0.018 0.001 PHE L 118 TYR 0.014 0.001 TYR H 111 ARG 0.003 0.000 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.02727 ( 180) hydrogen bonds : angle 6.13010 ( 471) SS BOND : bond 0.00330 ( 12) SS BOND : angle 0.95393 ( 24) covalent geometry : bond 0.00260 ( 8588) covalent geometry : angle 0.56890 (11689) *********************** 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: 49 poor density : 206 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.7809 (mp) cc_final: 0.6803 (tt) REVERT: H 52 ASN cc_start: 0.8287 (t0) cc_final: 0.8024 (t0) REVERT: H 85 SER cc_start: 0.7452 (t) cc_final: 0.6985 (p) REVERT: H 96 CYS cc_start: 0.5134 (p) cc_final: 0.3547 (p) REVERT: H 117 LEU cc_start: 0.8274 (tp) cc_final: 0.7987 (tp) REVERT: H 160 SER cc_start: 0.8012 (p) cc_final: 0.7774 (t) REVERT: H 172 THR cc_start: 0.8451 (m) cc_final: 0.7920 (p) REVERT: H 176 VAL cc_start: 0.7806 (t) cc_final: 0.7417 (p) REVERT: H 189 VAL cc_start: 0.8564 (t) cc_final: 0.8214 (p) REVERT: H 200 THR cc_start: 0.8559 (m) cc_final: 0.8214 (t) REVERT: H 201 TYR cc_start: 0.6311 (m-80) cc_final: 0.6048 (m-80) REVERT: L 46 LEU cc_start: 0.8167 (tp) cc_final: 0.7958 (tp) REVERT: L 83 PHE cc_start: 0.7458 (m-80) cc_final: 0.7121 (m-80) REVERT: L 97 MET cc_start: 0.6294 (mtm) cc_final: 0.5960 (mtm) REVERT: L 164 SER cc_start: 0.8492 (t) cc_final: 0.8168 (p) REVERT: L 178 SER cc_start: 0.8346 (t) cc_final: 0.7556 (m) REVERT: L 188 TYR cc_start: 0.7145 (t80) cc_final: 0.6865 (t80) REVERT: A 59 PHE cc_start: 0.6924 (m-10) cc_final: 0.6667 (m-10) REVERT: A 269 TYR cc_start: 0.7681 (m-80) cc_final: 0.7421 (m-80) REVERT: A 298 GLU cc_start: 0.7356 (tt0) cc_final: 0.7072 (tt0) REVERT: A 320 VAL cc_start: 0.5180 (m) cc_final: 0.4893 (t) REVERT: A 345 THR cc_start: 0.7130 (p) cc_final: 0.6871 (t) REVERT: A 353 TRP cc_start: 0.8068 (p-90) cc_final: 0.7607 (p-90) REVERT: A 357 ARG cc_start: 0.7647 (ptm-80) cc_final: 0.7148 (ptm-80) REVERT: A 369 TYR cc_start: 0.7297 (m-80) cc_final: 0.7075 (m-10) REVERT: A 378 LYS cc_start: 0.8106 (ptpp) cc_final: 0.7790 (ptpp) REVERT: A 382 VAL cc_start: 0.6089 (OUTLIER) cc_final: 0.5209 (p) REVERT: A 394 ASN cc_start: 0.6674 (t0) cc_final: 0.5991 (t0) REVERT: A 406 GLU cc_start: 0.7480 (pt0) cc_final: 0.7213 (pt0) REVERT: A 424 LYS cc_start: 0.7802 (ttmm) cc_final: 0.7484 (ttmm) REVERT: A 436 TRP cc_start: 0.7361 (p90) cc_final: 0.6772 (p90) REVERT: A 448 ASN cc_start: 0.7060 (m-40) cc_final: 0.6758 (m-40) REVERT: A 460 LYS cc_start: 0.8182 (mptm) cc_final: 0.7702 (mptm) REVERT: A 465 GLU cc_start: 0.6926 (tt0) cc_final: 0.6411 (tt0) REVERT: A 493 GLN cc_start: 0.6357 (tp40) cc_final: 0.5891 (tp40) REVERT: A 510 VAL cc_start: 0.8071 (t) cc_final: 0.7834 (m) REVERT: A 542 ASN cc_start: 0.6918 (t0) cc_final: 0.6705 (t0) REVERT: A 592 PHE cc_start: 0.1453 (OUTLIER) cc_final: -0.0449 (m-10) REVERT: A 697 MET cc_start: -0.4700 (ptp) cc_final: -0.5568 (ptt) outliers start: 49 outliers final: 36 residues processed: 238 average time/residue: 0.2131 time to fit residues: 68.3179 Evaluate side-chains 241 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 203 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 103 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 111 THR Chi-restraints excluded: chain L residue 142 TYR Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain A residue 57 LEU 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 299 THR Chi-restraints excluded: chain A residue 307 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 395 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 459 SER 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 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: 3.9990 chunk 72 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 87 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 61 optimal weight: 0.0270 chunk 46 optimal weight: 0.9990 chunk 60 optimal weight: 0.0870 overall best weight: 0.4218 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.214442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.180769 restraints weight = 18191.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.186103 restraints weight = 9706.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.189559 restraints weight = 5881.170| |-----------------------------------------------------------------------------| r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5854 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8600 Z= 0.104 Angle : 0.577 10.136 11713 Z= 0.286 Chirality : 0.044 0.156 1302 Planarity : 0.004 0.051 1507 Dihedral : 6.804 87.381 1201 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 5.22 % Allowed : 16.93 % 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: -2.58 (0.25), residues: 1065 helix: -1.28 (0.88), residues: 32 sheet: -0.87 (0.30), residues: 312 loop : -2.27 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 150 HIS 0.002 0.000 HIS L 90 PHE 0.016 0.001 PHE A 392 TYR 0.027 0.001 TYR H 35 ARG 0.002 0.000 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.02629 ( 180) hydrogen bonds : angle 5.92013 ( 471) SS BOND : bond 0.00293 ( 12) SS BOND : angle 0.92537 ( 24) covalent geometry : bond 0.00251 ( 8588) covalent geometry : angle 0.57618 (11689) *********************** 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 250 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.7790 (mp) cc_final: 0.6753 (tt) REVERT: H 6 GLN cc_start: 0.6701 (tt0) cc_final: 0.6463 (tt0) REVERT: H 39 GLN cc_start: 0.7640 (tp40) cc_final: 0.6979 (tt0) REVERT: H 52 ASN cc_start: 0.8291 (t0) cc_final: 0.8012 (t0) REVERT: H 85 SER cc_start: 0.7409 (t) cc_final: 0.6962 (p) REVERT: H 96 CYS cc_start: 0.5064 (p) cc_final: 0.3626 (p) REVERT: H 117 LEU cc_start: 0.8282 (tp) cc_final: 0.7975 (tp) REVERT: H 172 THR cc_start: 0.8441 (m) cc_final: 0.7917 (p) REVERT: H 176 VAL cc_start: 0.7811 (t) cc_final: 0.7418 (p) REVERT: H 189 VAL cc_start: 0.8530 (t) cc_final: 0.8186 (p) REVERT: H 200 THR cc_start: 0.8539 (m) cc_final: 0.8204 (t) REVERT: H 201 TYR cc_start: 0.6287 (m-80) cc_final: 0.6014 (m-80) REVERT: L 27 GLN cc_start: 0.7777 (tt0) cc_final: 0.7512 (tt0) REVERT: L 83 PHE cc_start: 0.7444 (m-80) cc_final: 0.7115 (m-80) REVERT: L 97 MET cc_start: 0.6522 (mtm) cc_final: 0.6101 (mtm) REVERT: L 164 SER cc_start: 0.8488 (t) cc_final: 0.8162 (p) REVERT: L 168 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7336 (mt0) REVERT: L 178 SER cc_start: 0.8316 (t) cc_final: 0.7517 (m) REVERT: A 59 PHE cc_start: 0.6896 (m-10) cc_final: 0.6666 (m-10) REVERT: A 269 TYR cc_start: 0.7723 (m-80) cc_final: 0.7460 (m-80) REVERT: A 298 GLU cc_start: 0.7362 (tt0) cc_final: 0.7064 (tt0) REVERT: A 320 VAL cc_start: 0.5348 (m) cc_final: 0.5022 (t) REVERT: A 345 THR cc_start: 0.7136 (p) cc_final: 0.6874 (t) REVERT: A 353 TRP cc_start: 0.8076 (p-90) cc_final: 0.7578 (p-90) REVERT: A 357 ARG cc_start: 0.7677 (ptm-80) cc_final: 0.7142 (ptm-80) REVERT: A 378 LYS cc_start: 0.8063 (ptpp) cc_final: 0.7683 (ptpp) REVERT: A 382 VAL cc_start: 0.6109 (OUTLIER) cc_final: 0.5230 (p) REVERT: A 394 ASN cc_start: 0.6693 (t0) cc_final: 0.5831 (t0) REVERT: A 406 GLU cc_start: 0.7504 (pt0) cc_final: 0.7239 (pt0) REVERT: A 424 LYS cc_start: 0.7864 (ttmm) cc_final: 0.7547 (ttmm) REVERT: A 436 TRP cc_start: 0.7354 (p90) cc_final: 0.6793 (p90) REVERT: A 448 ASN cc_start: 0.7069 (m-40) cc_final: 0.6725 (m-40) REVERT: A 458 LYS cc_start: 0.8869 (ttmt) cc_final: 0.8554 (ttmm) REVERT: A 460 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7694 (mptm) REVERT: A 465 GLU cc_start: 0.6902 (tt0) cc_final: 0.6294 (tt0) REVERT: A 493 GLN cc_start: 0.6366 (tp40) cc_final: 0.5891 (tp40) REVERT: A 516 GLU cc_start: 0.7123 (pt0) cc_final: 0.6846 (pt0) REVERT: A 592 PHE cc_start: 0.1498 (OUTLIER) cc_final: -0.0500 (m-10) REVERT: A 697 MET cc_start: -0.4678 (ptp) cc_final: -0.5593 (ptt) outliers start: 49 outliers final: 36 residues processed: 230 average time/residue: 0.2161 time to fit residues: 66.9728 Evaluate side-chains 242 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 202 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 124 LYS 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 35 TRP 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 168 GLN Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 211 PHE Chi-restraints excluded: chain A residue 57 LEU 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 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 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 460 LYS Chi-restraints excluded: chain A residue 468 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 57 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 chunk 1 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 50 optimal weight: 0.0270 chunk 23 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 171 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.212479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.178711 restraints weight = 18206.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.184053 restraints weight = 9719.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.187395 restraints weight = 5918.961| |-----------------------------------------------------------------------------| r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5912 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8600 Z= 0.134 Angle : 0.592 8.696 11713 Z= 0.297 Chirality : 0.045 0.271 1302 Planarity : 0.004 0.060 1507 Dihedral : 6.908 87.429 1201 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 4.90 % Allowed : 17.47 % Favored : 77.64 % 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: -1.79 (0.79), residues: 38 sheet: -0.85 (0.30), residues: 314 loop : -2.21 (0.22), residues: 713 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 0.017 0.001 PHE L 118 TYR 0.019 0.001 TYR H 35 ARG 0.003 0.000 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.02802 ( 180) hydrogen bonds : angle 5.89494 ( 471) SS BOND : bond 0.00343 ( 12) SS BOND : angle 1.13246 ( 24) covalent geometry : bond 0.00315 ( 8588) covalent geometry : angle 0.59032 (11689) *********************** 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 259 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 213 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.7827 (mp) cc_final: 0.6809 (tt) REVERT: H 6 GLN cc_start: 0.6712 (tt0) cc_final: 0.6320 (tt0) REVERT: H 39 GLN cc_start: 0.7727 (tp40) cc_final: 0.7055 (tt0) REVERT: H 52 ASN cc_start: 0.8392 (t0) cc_final: 0.8152 (t0) REVERT: H 85 SER cc_start: 0.7384 (t) cc_final: 0.6941 (p) REVERT: H 96 CYS cc_start: 0.5099 (p) cc_final: 0.3903 (p) REVERT: H 116 THR cc_start: 0.7560 (m) cc_final: 0.7164 (p) REVERT: H 117 LEU cc_start: 0.8302 (tp) cc_final: 0.7991 (tp) REVERT: H 172 THR cc_start: 0.8454 (m) cc_final: 0.7935 (p) REVERT: H 176 VAL cc_start: 0.7862 (t) cc_final: 0.7478 (p) REVERT: H 189 VAL cc_start: 0.8589 (t) cc_final: 0.8230 (p) REVERT: H 200 THR cc_start: 0.8644 (m) cc_final: 0.8297 (t) REVERT: H 201 TYR cc_start: 0.6249 (m-80) cc_final: 0.6001 (m-80) REVERT: L 14 SER cc_start: 0.8545 (m) cc_final: 0.8288 (t) REVERT: L 27 GLN cc_start: 0.7778 (tt0) cc_final: 0.7533 (tt0) REVERT: L 83 PHE cc_start: 0.7433 (m-80) cc_final: 0.7155 (m-80) REVERT: L 97 MET cc_start: 0.6473 (mtm) cc_final: 0.6118 (mtm) REVERT: L 164 SER cc_start: 0.8494 (t) cc_final: 0.8178 (p) REVERT: L 178 SER cc_start: 0.8293 (t) cc_final: 0.7567 (m) REVERT: A 59 PHE cc_start: 0.6856 (m-10) cc_final: 0.6629 (m-10) REVERT: A 269 TYR cc_start: 0.7620 (m-80) cc_final: 0.7372 (m-80) REVERT: A 298 GLU cc_start: 0.7389 (tt0) cc_final: 0.7035 (tt0) REVERT: A 320 VAL cc_start: 0.5292 (m) cc_final: 0.4979 (t) REVERT: A 345 THR cc_start: 0.7162 (p) cc_final: 0.6913 (t) REVERT: A 353 TRP cc_start: 0.8117 (p-90) cc_final: 0.7648 (p-90) REVERT: A 357 ARG cc_start: 0.7649 (ptm-80) cc_final: 0.7080 (ptm-80) REVERT: A 382 VAL cc_start: 0.6241 (OUTLIER) cc_final: 0.5374 (p) REVERT: A 394 ASN cc_start: 0.6800 (t0) cc_final: 0.5986 (t0) REVERT: A 406 GLU cc_start: 0.7457 (pt0) cc_final: 0.7214 (pt0) REVERT: A 424 LYS cc_start: 0.7942 (ttmm) cc_final: 0.7643 (ttmm) REVERT: A 436 TRP cc_start: 0.7379 (p90) cc_final: 0.6824 (p90) REVERT: A 448 ASN cc_start: 0.7153 (m-40) cc_final: 0.6835 (m-40) REVERT: A 458 LYS cc_start: 0.8825 (ttmt) cc_final: 0.8584 (ttmm) REVERT: A 460 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7747 (mptm) REVERT: A 465 GLU cc_start: 0.6885 (tt0) cc_final: 0.6316 (tt0) REVERT: A 510 VAL cc_start: 0.8237 (t) cc_final: 0.7931 (m) REVERT: A 516 GLU cc_start: 0.7094 (pt0) cc_final: 0.6871 (pt0) REVERT: A 592 PHE cc_start: 0.1572 (OUTLIER) cc_final: -0.0937 (m-10) REVERT: A 697 MET cc_start: -0.4521 (ptp) cc_final: -0.5485 (ptt) outliers start: 46 outliers final: 39 residues processed: 236 average time/residue: 0.2100 time to fit residues: 67.0407 Evaluate side-chains 252 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 210 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 124 LYS 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 35 TRP 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 177 LEU 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 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 390 LEU 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 459 SER Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 468 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 19 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 95 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 85 optimal weight: 0.0870 chunk 89 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 171 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.212626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.179089 restraints weight = 18183.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.184403 restraints weight = 9726.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.187763 restraints weight = 5911.874| |-----------------------------------------------------------------------------| r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5911 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8600 Z= 0.119 Angle : 0.584 8.639 11713 Z= 0.293 Chirality : 0.044 0.162 1302 Planarity : 0.004 0.066 1507 Dihedral : 6.953 87.269 1201 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 4.90 % Allowed : 17.78 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.49 (0.25), residues: 1065 helix: -1.81 (0.79), residues: 38 sheet: -0.80 (0.30), residues: 312 loop : -2.18 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 150 HIS 0.002 0.000 HIS L 90 PHE 0.018 0.001 PHE L 118 TYR 0.018 0.001 TYR H 35 ARG 0.003 0.000 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.02715 ( 180) hydrogen bonds : angle 5.78150 ( 471) SS BOND : bond 0.00409 ( 12) SS BOND : angle 1.05747 ( 24) covalent geometry : bond 0.00284 ( 8588) covalent geometry : angle 0.58250 (11689) *********************** 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 260 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 214 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.7816 (mp) cc_final: 0.6835 (tt) REVERT: H 6 GLN cc_start: 0.6706 (tt0) cc_final: 0.6373 (tt0) REVERT: H 39 GLN cc_start: 0.7740 (tp40) cc_final: 0.7154 (tt0) REVERT: H 52 ASN cc_start: 0.8407 (t0) cc_final: 0.8144 (t0) REVERT: H 83 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8333 (tp) REVERT: H 85 SER cc_start: 0.7345 (t) cc_final: 0.6900 (p) REVERT: H 96 CYS cc_start: 0.5084 (p) cc_final: 0.4367 (p) REVERT: H 116 THR cc_start: 0.7546 (m) cc_final: 0.7178 (p) REVERT: H 117 LEU cc_start: 0.8311 (tp) cc_final: 0.8014 (tp) REVERT: H 172 THR cc_start: 0.8425 (m) cc_final: 0.7892 (p) REVERT: H 176 VAL cc_start: 0.7880 (t) cc_final: 0.7490 (p) REVERT: H 189 VAL cc_start: 0.8604 (t) cc_final: 0.8192 (p) REVERT: H 200 THR cc_start: 0.8636 (m) cc_final: 0.8310 (t) REVERT: H 201 TYR cc_start: 0.6216 (m-80) cc_final: 0.5969 (m-80) REVERT: L 4 LEU cc_start: 0.7391 (mt) cc_final: 0.6859 (tp) REVERT: L 14 SER cc_start: 0.8541 (m) cc_final: 0.8259 (t) REVERT: L 27 GLN cc_start: 0.7802 (tt0) cc_final: 0.7575 (tt0) REVERT: L 48 ILE cc_start: 0.7631 (mm) cc_final: 0.7399 (mm) REVERT: L 61 ARG cc_start: 0.7528 (ptt-90) cc_final: 0.7189 (ptt-90) REVERT: L 83 PHE cc_start: 0.7433 (m-80) cc_final: 0.7129 (m-80) REVERT: L 97 MET cc_start: 0.6465 (mtm) cc_final: 0.6217 (mtm) REVERT: L 164 SER cc_start: 0.8481 (t) cc_final: 0.8178 (p) REVERT: L 178 SER cc_start: 0.8341 (t) cc_final: 0.7637 (m) REVERT: A 59 PHE cc_start: 0.6817 (m-10) cc_final: 0.6600 (m-10) REVERT: A 269 TYR cc_start: 0.7633 (m-80) cc_final: 0.7386 (m-80) REVERT: A 298 GLU cc_start: 0.7321 (tt0) cc_final: 0.6937 (tt0) REVERT: A 320 VAL cc_start: 0.5351 (m) cc_final: 0.5028 (t) REVERT: A 353 TRP cc_start: 0.8099 (p-90) cc_final: 0.7665 (p-90) REVERT: A 357 ARG cc_start: 0.7664 (ptm-80) cc_final: 0.7103 (ptm-80) REVERT: A 375 PHE cc_start: 0.8240 (t80) cc_final: 0.8021 (t80) REVERT: A 378 LYS cc_start: 0.7948 (ptpp) cc_final: 0.7494 (pttm) REVERT: A 382 VAL cc_start: 0.6277 (OUTLIER) cc_final: 0.5398 (p) REVERT: A 394 ASN cc_start: 0.6798 (t0) cc_final: 0.6042 (t0) REVERT: A 406 GLU cc_start: 0.7468 (pt0) cc_final: 0.7191 (pt0) REVERT: A 424 LYS cc_start: 0.7945 (ttmm) cc_final: 0.7642 (ttmm) REVERT: A 436 TRP cc_start: 0.7425 (p90) cc_final: 0.6882 (p90) REVERT: A 448 ASN cc_start: 0.7138 (m-40) cc_final: 0.6823 (m-40) REVERT: A 458 LYS cc_start: 0.8822 (ttmt) cc_final: 0.8440 (ttmm) REVERT: A 460 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7749 (mptm) REVERT: A 465 GLU cc_start: 0.6934 (tt0) cc_final: 0.6385 (tt0) REVERT: A 510 VAL cc_start: 0.8240 (t) cc_final: 0.7969 (m) REVERT: A 516 GLU cc_start: 0.7160 (pt0) cc_final: 0.6772 (pt0) REVERT: A 518 LEU cc_start: 0.8494 (mt) cc_final: 0.8262 (mp) REVERT: A 592 PHE cc_start: 0.1715 (OUTLIER) cc_final: -0.0931 (m-10) REVERT: A 697 MET cc_start: -0.4262 (ptp) cc_final: -0.5389 (ptt) outliers start: 46 outliers final: 38 residues processed: 238 average time/residue: 0.2119 time to fit residues: 68.7848 Evaluate side-chains 253 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 211 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 124 LYS 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 35 TRP 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 211 PHE Chi-restraints excluded: chain A residue 57 LEU 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 305 SER 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 382 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 459 SER Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 468 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 98 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 73 optimal weight: 0.3980 chunk 60 optimal weight: 0.0980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 171 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.210381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.176897 restraints weight = 18127.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.182226 restraints weight = 9707.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.185615 restraints weight = 5931.109| |-----------------------------------------------------------------------------| r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5964 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 8600 Z= 0.148 Angle : 0.613 9.003 11713 Z= 0.312 Chirality : 0.045 0.252 1302 Planarity : 0.005 0.071 1507 Dihedral : 7.097 86.980 1201 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 4.90 % Allowed : 18.64 % Favored : 76.46 % 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: -2.55 (0.25), residues: 1065 helix: -2.38 (0.68), residues: 44 sheet: -0.91 (0.30), residues: 316 loop : -2.15 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 150 HIS 0.004 0.001 HIS L 191 PHE 0.015 0.002 PHE L 118 TYR 0.022 0.001 TYR L 175 ARG 0.002 0.000 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.02925 ( 180) hydrogen bonds : angle 5.89957 ( 471) SS BOND : bond 0.00339 ( 12) SS BOND : angle 1.06160 ( 24) covalent geometry : bond 0.00351 ( 8588) covalent geometry : angle 0.61153 (11689) *********************** 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 261 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 215 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.7800 (mp) cc_final: 0.7587 (mp) REVERT: H 6 GLN cc_start: 0.6815 (tt0) cc_final: 0.6372 (tt0) REVERT: H 39 GLN cc_start: 0.7791 (tp40) cc_final: 0.7124 (tt0) REVERT: H 83 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8424 (tp) REVERT: H 85 SER cc_start: 0.7426 (t) cc_final: 0.6968 (p) REVERT: H 116 THR cc_start: 0.7580 (m) cc_final: 0.7270 (p) REVERT: H 117 LEU cc_start: 0.8361 (tp) cc_final: 0.8082 (tp) REVERT: H 172 THR cc_start: 0.8415 (m) cc_final: 0.7875 (p) REVERT: H 176 VAL cc_start: 0.7920 (t) cc_final: 0.7543 (p) REVERT: H 189 VAL cc_start: 0.8738 (t) cc_final: 0.8291 (p) REVERT: H 200 THR cc_start: 0.8686 (m) cc_final: 0.8406 (t) REVERT: L 4 LEU cc_start: 0.7540 (mt) cc_final: 0.7044 (tp) REVERT: L 14 SER cc_start: 0.8575 (m) cc_final: 0.8300 (t) REVERT: L 48 ILE cc_start: 0.7643 (mm) cc_final: 0.7415 (mm) REVERT: L 61 ARG cc_start: 0.7540 (ptt-90) cc_final: 0.7230 (ptt-90) REVERT: L 83 PHE cc_start: 0.7452 (m-80) cc_final: 0.7161 (m-80) REVERT: L 97 MET cc_start: 0.6426 (mtm) cc_final: 0.6154 (mtm) REVERT: L 107 GLU cc_start: 0.7039 (mm-30) cc_final: 0.6545 (mm-30) REVERT: L 164 SER cc_start: 0.8484 (t) cc_final: 0.8133 (p) REVERT: L 178 SER cc_start: 0.8323 (t) cc_final: 0.7560 (m) REVERT: A 59 PHE cc_start: 0.6772 (m-10) cc_final: 0.6527 (m-10) REVERT: A 298 GLU cc_start: 0.7385 (tt0) cc_final: 0.6992 (tt0) REVERT: A 320 VAL cc_start: 0.5211 (m) cc_final: 0.4946 (t) REVERT: A 345 THR cc_start: 0.7209 (p) cc_final: 0.6976 (t) REVERT: A 353 TRP cc_start: 0.8175 (p-90) cc_final: 0.7687 (p-90) REVERT: A 357 ARG cc_start: 0.7662 (ptm-80) cc_final: 0.7356 (ptm-80) REVERT: A 382 VAL cc_start: 0.6449 (OUTLIER) cc_final: 0.5605 (p) REVERT: A 394 ASN cc_start: 0.6880 (t0) cc_final: 0.6483 (t0) REVERT: A 406 GLU cc_start: 0.7486 (pt0) cc_final: 0.7207 (pt0) REVERT: A 424 LYS cc_start: 0.8002 (ttmm) cc_final: 0.7690 (ttmm) REVERT: A 433 VAL cc_start: 0.7860 (p) cc_final: 0.7427 (m) REVERT: A 436 TRP cc_start: 0.7455 (p90) cc_final: 0.6804 (p90) REVERT: A 448 ASN cc_start: 0.7210 (m-40) cc_final: 0.6893 (m-40) REVERT: A 460 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7751 (mptm) REVERT: A 465 GLU cc_start: 0.6977 (tt0) cc_final: 0.6326 (tt0) REVERT: A 516 GLU cc_start: 0.7186 (pt0) cc_final: 0.6880 (pt0) REVERT: A 592 PHE cc_start: 0.2719 (OUTLIER) cc_final: -0.0548 (m-10) REVERT: A 697 MET cc_start: -0.4037 (ptp) cc_final: -0.4818 (ptt) outliers start: 46 outliers final: 38 residues processed: 239 average time/residue: 0.2109 time to fit residues: 68.8113 Evaluate side-chains 249 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 207 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 124 LYS Chi-restraints excluded: chain H residue 158 THR 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 35 TRP Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 211 PHE Chi-restraints excluded: chain A residue 57 LEU 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 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 390 LEU 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 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 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: 0.9980 chunk 51 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 19 optimal weight: 0.0470 chunk 11 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 73 optimal weight: 0.0000 chunk 5 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.5682 ------------------------------------------------------------------------------- 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 168 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.211627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.178490 restraints weight = 18207.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.183847 restraints weight = 9762.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.187210 restraints weight = 5958.197| |-----------------------------------------------------------------------------| r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5929 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8600 Z= 0.119 Angle : 0.613 8.453 11713 Z= 0.312 Chirality : 0.045 0.229 1302 Planarity : 0.005 0.079 1507 Dihedral : 7.073 86.825 1201 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 4.26 % Allowed : 19.38 % 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: -2.49 (0.25), residues: 1065 helix: -2.29 (0.69), residues: 43 sheet: -0.89 (0.31), residues: 311 loop : -2.08 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 150 HIS 0.002 0.001 HIS L 191 PHE 0.018 0.001 PHE L 118 TYR 0.014 0.001 TYR H 35 ARG 0.004 0.000 ARG L 144 Details of bonding type rmsd hydrogen bonds : bond 0.02698 ( 180) hydrogen bonds : angle 5.77270 ( 471) SS BOND : bond 0.00413 ( 12) SS BOND : angle 1.69954 ( 24) covalent geometry : bond 0.00283 ( 8588) covalent geometry : angle 0.60914 (11689) ********************** 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 252 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.7834 (mp) cc_final: 0.7349 (tt) REVERT: H 6 GLN cc_start: 0.6758 (tt0) cc_final: 0.6402 (tt0) REVERT: H 39 GLN cc_start: 0.7736 (tp40) cc_final: 0.7152 (tt0) REVERT: H 85 SER cc_start: 0.7327 (t) cc_final: 0.6879 (p) REVERT: H 116 THR cc_start: 0.7564 (m) cc_final: 0.7224 (p) REVERT: H 117 LEU cc_start: 0.8336 (tp) cc_final: 0.8061 (tp) REVERT: H 172 THR cc_start: 0.8404 (m) cc_final: 0.7873 (p) REVERT: H 176 VAL cc_start: 0.7892 (t) cc_final: 0.7517 (p) REVERT: H 189 VAL cc_start: 0.8676 (t) cc_final: 0.8227 (p) REVERT: H 200 THR cc_start: 0.8701 (m) cc_final: 0.8398 (t) REVERT: H 201 TYR cc_start: 0.6156 (m-80) cc_final: 0.5914 (m-80) REVERT: L 4 LEU cc_start: 0.7499 (mt) cc_final: 0.6994 (tp) REVERT: L 14 SER cc_start: 0.8518 (m) cc_final: 0.8246 (t) REVERT: L 48 ILE cc_start: 0.7673 (mm) cc_final: 0.7449 (mm) REVERT: L 83 PHE cc_start: 0.7426 (m-80) cc_final: 0.7105 (m-80) REVERT: L 97 MET cc_start: 0.6452 (mtm) cc_final: 0.6188 (mtm) REVERT: L 107 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6521 (mm-30) REVERT: L 147 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7351 (mppt) REVERT: L 164 SER cc_start: 0.8499 (t) cc_final: 0.8151 (p) REVERT: L 178 SER cc_start: 0.8334 (t) cc_final: 0.7618 (m) REVERT: A 59 PHE cc_start: 0.6686 (m-10) cc_final: 0.6473 (m-10) REVERT: A 298 GLU cc_start: 0.7315 (tt0) cc_final: 0.6975 (tt0) REVERT: A 319 ARG cc_start: 0.4447 (OUTLIER) cc_final: 0.3445 (mtm180) REVERT: A 320 VAL cc_start: 0.5471 (m) cc_final: 0.5137 (t) REVERT: A 353 TRP cc_start: 0.8142 (p-90) cc_final: 0.7682 (p-90) REVERT: A 382 VAL cc_start: 0.6456 (OUTLIER) cc_final: 0.5637 (p) REVERT: A 406 GLU cc_start: 0.7447 (pt0) cc_final: 0.7131 (pt0) REVERT: A 424 LYS cc_start: 0.7885 (ttmm) cc_final: 0.7543 (ttmm) REVERT: A 433 VAL cc_start: 0.7801 (p) cc_final: 0.7396 (m) REVERT: A 436 TRP cc_start: 0.7450 (p90) cc_final: 0.6852 (p90) REVERT: A 448 ASN cc_start: 0.7127 (m-40) cc_final: 0.6825 (m-40) REVERT: A 460 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7741 (mptm) REVERT: A 465 GLU cc_start: 0.6999 (tt0) cc_final: 0.6412 (tt0) REVERT: A 516 GLU cc_start: 0.7221 (pt0) cc_final: 0.6887 (pt0) REVERT: A 592 PHE cc_start: 0.2494 (OUTLIER) cc_final: -0.0635 (m-10) outliers start: 40 outliers final: 31 residues processed: 235 average time/residue: 0.2055 time to fit residues: 66.1081 Evaluate side-chains 247 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 211 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 168 SER 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 35 TRP Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 211 PHE Chi-restraints excluded: chain A residue 57 LEU 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 382 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 511 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 64 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 101 optimal weight: 0.2980 chunk 92 optimal weight: 0.0170 chunk 104 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 60 optimal weight: 0.0040 chunk 20 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.4232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 171 HIS A 70 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.212184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.179273 restraints weight = 18277.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.184591 restraints weight = 9738.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.187967 restraints weight = 5924.899| |-----------------------------------------------------------------------------| r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5911 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8600 Z= 0.108 Angle : 0.600 8.544 11713 Z= 0.303 Chirality : 0.045 0.226 1302 Planarity : 0.005 0.081 1507 Dihedral : 6.817 86.750 1197 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % 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: -2.33 (0.25), residues: 1065 helix: -1.15 (0.90), residues: 31 sheet: -0.83 (0.31), residues: 313 loop : -2.02 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 150 HIS 0.007 0.001 HIS A 67 PHE 0.024 0.001 PHE A 429 TYR 0.013 0.001 TYR H 35 ARG 0.005 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.02554 ( 180) hydrogen bonds : angle 5.58624 ( 471) SS BOND : bond 0.00312 ( 12) SS BOND : angle 1.14567 ( 24) covalent geometry : bond 0.00261 ( 8588) covalent geometry : angle 0.59789 (11689) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3457.09 seconds wall clock time: 60 minutes 24.75 seconds (3624.75 seconds total)