Starting phenix.real_space_refine on Fri Nov 15 06:02:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kej_37160/11_2024/8kej_37160.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kej_37160/11_2024/8kej_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kej_37160/11_2024/8kej_37160.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kej_37160/11_2024/8kej_37160.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kej_37160/11_2024/8kej_37160.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kej_37160/11_2024/8kej_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 5.13, per 1000 atoms: 0.61 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: 2.16 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: 1.06 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: 2.49 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2594 1.34 - 1.45: 1450 1.45 - 1.57: 4501 1.57 - 1.69: 0 1.69 - 1.81: 43 Bond restraints: 8588 Sorted by residual: bond pdb=" N GLU L 145 " pdb=" CA GLU L 145 " ideal model delta sigma weight residual 1.459 1.488 -0.028 9.10e-03 1.21e+04 9.65e+00 bond pdb=" N VAL A 595 " pdb=" CA VAL A 595 " ideal model delta sigma weight residual 1.460 1.493 -0.034 1.10e-02 8.26e+03 9.42e+00 bond pdb=" N ASN L 139 " pdb=" CA ASN L 139 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.23e-02 6.61e+03 8.76e+00 bond pdb=" N LEU A 585 " pdb=" CA LEU A 585 " ideal model delta sigma weight residual 1.455 1.489 -0.035 1.25e-02 6.40e+03 7.65e+00 bond pdb=" N ARG L 144 " pdb=" CA ARG L 144 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.96e+00 ... (remaining 8583 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 10981 1.24 - 2.49: 542 2.49 - 3.73: 137 3.73 - 4.98: 22 4.98 - 6.22: 7 Bond angle restraints: 11689 Sorted by residual: angle pdb=" CA PHE L 141 " pdb=" CB PHE L 141 " pdb=" CG PHE L 141 " ideal model delta sigma weight residual 113.80 117.84 -4.04 1.00e+00 1.00e+00 1.64e+01 angle pdb=" N GLU L 145 " pdb=" CA GLU L 145 " pdb=" C GLU L 145 " ideal model delta sigma weight residual 112.99 106.78 6.21 1.61e+00 3.86e-01 1.49e+01 angle pdb=" C TYR L 142 " pdb=" N PRO L 143 " pdb=" CA PRO L 143 " ideal model delta sigma weight residual 119.84 124.53 -4.69 1.25e+00 6.40e-01 1.41e+01 angle pdb=" C PHE H 102 " pdb=" N ILE H 103 " pdb=" CA ILE H 103 " ideal model delta sigma weight residual 120.43 123.97 -3.54 9.60e-01 1.09e+00 1.36e+01 angle pdb=" CA TYR L 142 " pdb=" C TYR L 142 " pdb=" O TYR L 142 " ideal model delta sigma weight residual 120.87 116.94 3.93 1.10e+00 8.26e-01 1.28e+01 ... (remaining 11684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 4840 17.31 - 34.63: 212 34.63 - 51.94: 39 51.94 - 69.25: 9 69.25 - 86.56: 1 Dihedral angle restraints: 5101 sinusoidal: 1970 harmonic: 3131 Sorted by residual: dihedral pdb=" CA PRO A 589 " pdb=" C PRO A 589 " pdb=" N CYS A 590 " pdb=" CA CYS A 590 " ideal model delta harmonic sigma weight residual 180.00 -155.63 -24.37 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CB GLU A 281 " pdb=" CG GLU A 281 " pdb=" CD GLU A 281 " pdb=" OE1 GLU A 281 " ideal model delta sinusoidal sigma weight residual 0.00 86.56 -86.56 1 3.00e+01 1.11e-03 1.00e+01 dihedral pdb=" CG ARG L 144 " pdb=" CD ARG L 144 " pdb=" NE ARG L 144 " pdb=" CZ ARG L 144 " ideal model delta sinusoidal sigma weight residual -180.00 -136.73 -43.27 2 1.50e+01 4.44e-03 1.00e+01 ... (remaining 5098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1087 0.055 - 0.110: 197 0.110 - 0.165: 15 0.165 - 0.220: 2 0.220 - 0.275: 1 Chirality restraints: 1302 Sorted by residual: chirality pdb=" CA LEU A 585 " pdb=" N LEU A 585 " pdb=" C LEU A 585 " pdb=" CB LEU A 585 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA GLU L 145 " pdb=" N GLU L 145 " pdb=" C GLU L 145 " pdb=" CB GLU L 145 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.34e-01 chirality pdb=" CA LYS L 147 " pdb=" N LYS L 147 " pdb=" C LYS L 147 " pdb=" CB LYS L 147 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.44e-01 ... (remaining 1299 not shown) Planarity restraints: 1507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO A 521 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 462 " 0.019 5.00e-02 4.00e+02 2.89e-02 1.33e+00 pdb=" N PRO A 463 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 329 " -0.019 5.00e-02 4.00e+02 2.81e-02 1.27e+00 pdb=" N PRO A 330 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 330 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 330 " -0.016 5.00e-02 4.00e+02 ... (remaining 1504 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1685 2.78 - 3.31: 7447 3.31 - 3.84: 13495 3.84 - 4.37: 15093 4.37 - 4.90: 26493 Nonbonded interactions: 64213 Sorted by model distance: nonbonded pdb=" OE1 GLU L 107 " pdb=" OH TYR L 175 " model vdw 2.252 3.040 nonbonded pdb=" OG1 THR A 430 " pdb=" O PHE A 515 " model vdw 2.277 3.040 nonbonded pdb=" OH TYR L 32 " pdb=" OD1 ASP A 428 " model vdw 2.283 3.040 nonbonded pdb=" O VAL H 149 " pdb=" OG SER H 184 " model vdw 2.291 3.040 nonbonded pdb=" O TYR L 188 " pdb=" OH TYR L 194 " model vdw 2.299 3.040 ... (remaining 64208 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.440 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5604 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8588 Z= 0.191 Angle : 0.653 6.219 11689 Z= 0.417 Chirality : 0.042 0.275 1302 Planarity : 0.003 0.033 1507 Dihedral : 9.634 86.563 3059 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.70 % Favored : 92.11 % Rotamer: Outliers : 5.75 % Allowed : 7.35 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.21), residues: 1065 helix: -2.47 (0.70), residues: 31 sheet: -2.40 (0.25), residues: 322 loop : -3.20 (0.19), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP A 353 HIS 0.001 0.000 HIS L 90 PHE 0.018 0.001 PHE L 141 TYR 0.007 0.001 TYR L 142 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 228 time to evaluate : 0.916 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: 0.2215 time to fit residues: 78.6431 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 : 0.949 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5772 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 8588 Z= 0.220 Angle : 0.607 10.588 11689 Z= 0.311 Chirality : 0.045 0.168 1302 Planarity : 0.005 0.055 1507 Dihedral : 7.084 87.745 1217 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 4.69 % Allowed : 12.46 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.22), residues: 1065 helix: -1.49 (0.87), residues: 25 sheet: -1.76 (0.27), residues: 318 loop : -2.84 (0.20), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 94 HIS 0.003 0.001 HIS A 245 PHE 0.017 0.001 PHE A 377 TYR 0.017 0.001 TYR A 265 ARG 0.003 0.000 ARG L 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 217 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.7746 (mp) cc_final: 0.7087 (tt) REVERT: H 68 VAL cc_start: 0.8459 (OUTLIER) cc_final: 0.8051 (t) REVERT: H 85 SER cc_start: 0.7704 (t) cc_final: 0.7275 (p) REVERT: H 103 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.6148 (mt) REVERT: H 117 LEU cc_start: 0.8211 (tp) cc_final: 0.7996 (tp) REVERT: H 148 LEU cc_start: 0.8118 (tt) cc_final: 0.7886 (tt) REVERT: H 160 SER cc_start: 0.7935 (p) cc_final: 0.7656 (t) REVERT: H 176 VAL cc_start: 0.7742 (t) cc_final: 0.7306 (p) REVERT: H 189 VAL cc_start: 0.8617 (t) cc_final: 0.8214 (p) REVERT: H 200 THR cc_start: 0.8491 (m) cc_final: 0.8152 (t) REVERT: H 201 TYR cc_start: 0.6386 (m-80) cc_final: 0.6115 (m-80) REVERT: L 11 LEU cc_start: 0.7616 (tp) cc_final: 0.7381 (mm) REVERT: L 46 LEU cc_start: 0.8040 (tp) cc_final: 0.7728 (tp) REVERT: L 83 PHE cc_start: 0.7397 (m-80) cc_final: 0.7075 (m-80) REVERT: L 97 MET cc_start: 0.6172 (mtm) cc_final: 0.5668 (mtm) REVERT: L 164 SER cc_start: 0.8447 (t) cc_final: 0.8024 (p) REVERT: L 178 SER cc_start: 0.8291 (t) cc_final: 0.7483 (m) REVERT: A 57 LEU cc_start: 0.7423 (tp) cc_final: 0.7136 (tp) REVERT: A 59 PHE cc_start: 0.7215 (m-10) cc_final: 0.6994 (m-10) REVERT: A 269 TYR cc_start: 0.7656 (m-80) cc_final: 0.7412 (m-80) REVERT: A 298 GLU cc_start: 0.7301 (tt0) cc_final: 0.7091 (tt0) REVERT: A 310 LYS cc_start: 0.7413 (mtmt) cc_final: 0.6919 (ptpp) REVERT: A 357 ARG cc_start: 0.7523 (ptm-80) cc_final: 0.7297 (ptm-80) REVERT: A 378 LYS cc_start: 0.8014 (ptpp) cc_final: 0.7582 (pttm) REVERT: A 382 VAL cc_start: 0.5911 (OUTLIER) cc_final: 0.4994 (p) REVERT: A 436 TRP cc_start: 0.7245 (p90) cc_final: 0.6807 (p90) REVERT: A 448 ASN cc_start: 0.6950 (m110) cc_final: 0.6624 (m-40) REVERT: A 460 LYS cc_start: 0.8158 (mptm) cc_final: 0.7726 (mptm) REVERT: A 510 VAL cc_start: 0.8209 (t) cc_final: 0.7985 (m) REVERT: A 542 ASN cc_start: 0.6951 (t0) cc_final: 0.6709 (t0) REVERT: A 592 PHE cc_start: 0.1094 (OUTLIER) cc_final: -0.0459 (m-10) REVERT: A 697 MET cc_start: -0.4724 (ptp) cc_final: -0.5719 (ptt) outliers start: 44 outliers final: 27 residues processed: 251 average time/residue: 0.2187 time to fit residues: 73.5499 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 : 1.006 ------------------------------------------------------------------------------- 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 53 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 80 optimal weight: 0.0040 chunk 65 optimal weight: 0.8980 chunk 26 optimal weight: 0.0970 chunk 96 optimal weight: 0.1980 chunk 104 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5775 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8588 Z= 0.163 Angle : 0.563 10.270 11689 Z= 0.288 Chirality : 0.044 0.169 1302 Planarity : 0.004 0.049 1507 Dihedral : 6.841 87.794 1206 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 4.26 % Allowed : 14.70 % Favored : 81.04 % 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: -3.23 (0.23), residues: 1065 helix: -1.79 (0.82), residues: 26 sheet: -1.47 (0.28), residues: 336 loop : -2.66 (0.21), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP L 150 HIS 0.002 0.001 HIS H 207 PHE 0.019 0.001 PHE H 129 TYR 0.014 0.001 TYR H 35 ARG 0.003 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 198 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.7794 (mp) cc_final: 0.7059 (tt) REVERT: H 34 MET cc_start: 0.7071 (mmm) cc_final: 0.6826 (mmm) REVERT: H 85 SER cc_start: 0.7605 (t) cc_final: 0.7138 (p) REVERT: H 160 SER cc_start: 0.7955 (p) cc_final: 0.7696 (t) REVERT: H 176 VAL cc_start: 0.7809 (t) cc_final: 0.7401 (p) REVERT: H 189 VAL cc_start: 0.8498 (t) cc_final: 0.8128 (p) REVERT: H 200 THR cc_start: 0.8484 (m) cc_final: 0.8140 (t) REVERT: H 201 TYR cc_start: 0.6376 (m-80) cc_final: 0.6110 (m-80) REVERT: L 46 LEU cc_start: 0.8085 (tp) cc_final: 0.7783 (tp) REVERT: L 83 PHE cc_start: 0.7372 (m-80) cc_final: 0.7072 (m-80) REVERT: L 97 MET cc_start: 0.6195 (mtm) cc_final: 0.5814 (mtm) REVERT: L 164 SER cc_start: 0.8486 (t) cc_final: 0.8100 (p) REVERT: L 178 SER cc_start: 0.8268 (t) cc_final: 0.7405 (m) REVERT: L 188 TYR cc_start: 0.7218 (t80) cc_final: 0.7004 (t80) REVERT: A 57 LEU cc_start: 0.7455 (tp) cc_final: 0.7121 (tp) REVERT: A 59 PHE cc_start: 0.7147 (m-10) cc_final: 0.6938 (m-10) REVERT: A 269 TYR cc_start: 0.7717 (m-80) cc_final: 0.7420 (m-80) REVERT: A 298 GLU cc_start: 0.7347 (tt0) cc_final: 0.7103 (tt0) REVERT: A 310 LYS cc_start: 0.7528 (mtmt) cc_final: 0.6580 (ptpt) REVERT: A 378 LYS cc_start: 0.8032 (ptpp) cc_final: 0.7726 (ptpp) REVERT: A 382 VAL cc_start: 0.5904 (OUTLIER) cc_final: 0.4957 (p) REVERT: A 406 GLU cc_start: 0.7507 (pt0) cc_final: 0.7137 (pt0) REVERT: A 436 TRP cc_start: 0.7256 (p90) cc_final: 0.6795 (p90) REVERT: A 448 ASN cc_start: 0.6953 (m110) cc_final: 0.6617 (m-40) REVERT: A 460 LYS cc_start: 0.8209 (mptm) cc_final: 0.7759 (mptm) REVERT: A 465 GLU cc_start: 0.6861 (tt0) cc_final: 0.6338 (tt0) REVERT: A 539 VAL cc_start: 0.7522 (t) cc_final: 0.7252 (p) REVERT: A 542 ASN cc_start: 0.6937 (t0) cc_final: 0.6697 (t0) REVERT: A 592 PHE cc_start: 0.0995 (OUTLIER) cc_final: -0.0626 (m-10) REVERT: A 697 MET cc_start: -0.5050 (ptp) cc_final: -0.5830 (ptt) outliers start: 40 outliers final: 30 residues processed: 224 average time/residue: 0.2295 time to fit residues: 68.9693 Evaluate side-chains 224 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 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 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 95 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 50 optimal weight: 0.0770 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 0.0370 chunk 64 optimal weight: 0.0020 chunk 96 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 overall best weight: 0.3024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 171 HIS A 314 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5772 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8588 Z= 0.152 Angle : 0.549 8.946 11689 Z= 0.276 Chirality : 0.044 0.180 1302 Planarity : 0.004 0.052 1507 Dihedral : 6.767 87.862 1205 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 4.37 % Allowed : 15.76 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.24), residues: 1065 helix: -1.34 (0.86), residues: 26 sheet: -1.24 (0.28), residues: 335 loop : -2.55 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 150 HIS 0.003 0.001 HIS L 200 PHE 0.021 0.001 PHE A 374 TYR 0.011 0.001 TYR H 60 ARG 0.005 0.000 ARG A 357 *********************** 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 239 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 0.862 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: 0.6754 (tt) REVERT: H 58 VAL cc_start: 0.8155 (m) cc_final: 0.7184 (t) REVERT: H 68 VAL cc_start: 0.8464 (OUTLIER) cc_final: 0.8223 (t) REVERT: H 85 SER cc_start: 0.7483 (t) cc_final: 0.7040 (p) REVERT: H 96 CYS cc_start: 0.5080 (p) cc_final: 0.3420 (p) REVERT: H 160 SER cc_start: 0.7948 (p) cc_final: 0.7668 (t) REVERT: H 176 VAL cc_start: 0.7851 (t) cc_final: 0.7454 (p) REVERT: H 200 THR cc_start: 0.8476 (m) cc_final: 0.8145 (t) REVERT: H 201 TYR cc_start: 0.6357 (m-80) cc_final: 0.6098 (m-80) REVERT: L 46 LEU cc_start: 0.8115 (tp) cc_final: 0.7870 (tp) REVERT: L 83 PHE cc_start: 0.7334 (m-80) cc_final: 0.7040 (m-80) REVERT: L 97 MET cc_start: 0.6192 (mtm) cc_final: 0.5967 (mtm) REVERT: L 164 SER cc_start: 0.8538 (t) cc_final: 0.8176 (p) REVERT: L 168 GLN cc_start: 0.7795 (tt0) cc_final: 0.7340 (mt0) REVERT: L 178 SER cc_start: 0.8253 (t) cc_final: 0.7432 (m) REVERT: A 57 LEU cc_start: 0.7485 (tp) cc_final: 0.7106 (tp) REVERT: A 269 TYR cc_start: 0.7696 (m-80) cc_final: 0.7402 (m-80) REVERT: A 298 GLU cc_start: 0.7338 (tt0) cc_final: 0.7107 (tt0) REVERT: A 310 LYS cc_start: 0.7501 (mtmt) cc_final: 0.6618 (ptmt) REVERT: A 378 LYS cc_start: 0.7970 (ptpp) cc_final: 0.7560 (pttm) REVERT: A 382 VAL cc_start: 0.5897 (OUTLIER) cc_final: 0.4959 (p) REVERT: A 406 GLU cc_start: 0.7553 (pt0) cc_final: 0.7231 (pt0) REVERT: A 424 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7663 (ttmm) REVERT: A 436 TRP cc_start: 0.7200 (p90) cc_final: 0.6752 (p90) REVERT: A 448 ASN cc_start: 0.6947 (m110) cc_final: 0.6602 (m-40) REVERT: A 460 LYS cc_start: 0.8221 (mptm) cc_final: 0.7776 (mptm) REVERT: A 465 GLU cc_start: 0.6911 (tt0) cc_final: 0.6343 (tt0) REVERT: A 478 LYS cc_start: 0.7708 (mmmt) cc_final: 0.7480 (mmmm) REVERT: A 539 VAL cc_start: 0.7524 (t) cc_final: 0.7291 (p) REVERT: A 542 ASN cc_start: 0.6799 (t0) cc_final: 0.6577 (t0) REVERT: A 592 PHE cc_start: 0.0868 (OUTLIER) cc_final: -0.0797 (m-80) REVERT: A 697 MET cc_start: -0.5089 (ptp) cc_final: -0.5817 (ptt) outliers start: 41 outliers final: 32 residues processed: 225 average time/residue: 0.2233 time to fit residues: 67.9316 Evaluate side-chains 231 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 H residue 158 THR Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 142 TYR Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 354 ASN 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 424 LYS Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 585 LEU 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 58 optimal weight: 3.9990 chunk 1 optimal weight: 0.0040 chunk 76 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 87 optimal weight: 0.0010 chunk 70 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 34 optimal weight: 8.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 107 ASN A 188 ASN A 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5848 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8588 Z= 0.190 Angle : 0.572 9.923 11689 Z= 0.287 Chirality : 0.044 0.186 1302 Planarity : 0.004 0.053 1507 Dihedral : 6.862 87.979 1204 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 5.64 % Allowed : 15.76 % Favored : 78.59 % 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: -2.79 (0.24), residues: 1065 helix: -0.80 (0.93), residues: 26 sheet: -1.04 (0.30), residues: 314 loop : -2.43 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 150 HIS 0.002 0.001 HIS L 191 PHE 0.017 0.001 PHE A 60 TYR 0.015 0.001 TYR A 265 ARG 0.002 0.000 ARG A 357 *********************** 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 261 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 208 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLN cc_start: 0.6657 (tt0) cc_final: 0.6388 (tt0) REVERT: H 34 MET cc_start: 0.7395 (mmm) cc_final: 0.7154 (mmm) REVERT: H 36 TRP cc_start: 0.7244 (t-100) cc_final: 0.6783 (m-90) REVERT: H 68 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8322 (t) REVERT: H 85 SER cc_start: 0.7447 (t) cc_final: 0.7001 (p) REVERT: H 96 CYS cc_start: 0.5018 (p) cc_final: 0.4674 (p) REVERT: H 117 LEU cc_start: 0.8272 (tp) cc_final: 0.8024 (tp) REVERT: H 176 VAL cc_start: 0.7875 (t) cc_final: 0.7492 (p) REVERT: H 189 VAL cc_start: 0.8512 (t) cc_final: 0.8171 (p) REVERT: H 200 THR cc_start: 0.8512 (m) cc_final: 0.8180 (t) REVERT: H 201 TYR cc_start: 0.6318 (m-80) cc_final: 0.6057 (m-80) REVERT: L 46 LEU cc_start: 0.8153 (tp) cc_final: 0.7914 (tp) REVERT: L 83 PHE cc_start: 0.7353 (m-80) cc_final: 0.7053 (m-80) REVERT: L 97 MET cc_start: 0.6246 (mtm) cc_final: 0.5934 (mtm) REVERT: L 164 SER cc_start: 0.8419 (t) cc_final: 0.8127 (p) REVERT: L 168 GLN cc_start: 0.7851 (tt0) cc_final: 0.7392 (mt0) REVERT: L 178 SER cc_start: 0.8336 (t) cc_final: 0.7526 (m) REVERT: L 188 TYR cc_start: 0.7324 (t80) cc_final: 0.7032 (t80) REVERT: A 269 TYR cc_start: 0.7743 (m-80) cc_final: 0.7450 (m-80) REVERT: A 298 GLU cc_start: 0.7426 (tt0) cc_final: 0.7188 (tt0) REVERT: A 310 LYS cc_start: 0.7643 (mtmt) cc_final: 0.6810 (ptmt) REVERT: A 345 THR cc_start: 0.7200 (p) cc_final: 0.6935 (t) REVERT: A 353 TRP cc_start: 0.8061 (p-90) cc_final: 0.7570 (p-90) REVERT: A 357 ARG cc_start: 0.7711 (ptm-80) cc_final: 0.7264 (ptm-80) REVERT: A 378 LYS cc_start: 0.8095 (ptpp) cc_final: 0.7798 (ptpp) REVERT: A 382 VAL cc_start: 0.6038 (OUTLIER) cc_final: 0.5133 (p) REVERT: A 406 GLU cc_start: 0.7503 (pt0) cc_final: 0.7224 (pt0) REVERT: A 424 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7589 (ttmm) REVERT: A 436 TRP cc_start: 0.7285 (p90) cc_final: 0.6700 (p90) REVERT: A 448 ASN cc_start: 0.7063 (m110) cc_final: 0.6698 (m-40) REVERT: A 460 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7758 (mptm) REVERT: A 465 GLU cc_start: 0.6932 (tt0) cc_final: 0.6426 (tt0) REVERT: A 510 VAL cc_start: 0.8359 (p) cc_final: 0.7944 (m) REVERT: A 518 LEU cc_start: 0.8662 (mp) cc_final: 0.8357 (mp) REVERT: A 539 VAL cc_start: 0.7762 (t) cc_final: 0.7534 (p) REVERT: A 542 ASN cc_start: 0.6913 (t0) cc_final: 0.6711 (t0) REVERT: A 592 PHE cc_start: 0.1584 (OUTLIER) cc_final: 0.0075 (m-10) REVERT: A 697 MET cc_start: -0.4715 (ptp) cc_final: -0.5481 (ptt) outliers start: 53 outliers final: 36 residues processed: 243 average time/residue: 0.2182 time to fit residues: 71.2717 Evaluate side-chains 242 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 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 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 149 GLN Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 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 424 LYS 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 551 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 596 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.0060 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 33 optimal weight: 0.0870 chunk 53 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 126 GLN A 70 HIS A 448 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5895 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 8588 Z= 0.219 Angle : 0.596 8.337 11689 Z= 0.298 Chirality : 0.045 0.179 1302 Planarity : 0.004 0.055 1507 Dihedral : 6.995 87.638 1204 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 5.75 % Allowed : 16.19 % Favored : 78.06 % 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: -2.68 (0.25), residues: 1065 helix: -1.59 (0.82), residues: 32 sheet: -0.95 (0.30), residues: 314 loop : -2.32 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 150 HIS 0.009 0.001 HIS A 67 PHE 0.035 0.002 PHE H 29 TYR 0.017 0.001 TYR H 60 ARG 0.002 0.000 ARG L 213 *********************** 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 263 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 209 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.7763 (mp) cc_final: 0.6877 (tt) REVERT: H 6 GLN cc_start: 0.6696 (tt0) cc_final: 0.6308 (tt0) REVERT: H 39 GLN cc_start: 0.7835 (tp40) cc_final: 0.6943 (tp40) REVERT: H 85 SER cc_start: 0.7442 (t) cc_final: 0.6999 (p) REVERT: H 96 CYS cc_start: 0.4972 (p) cc_final: 0.3654 (p) REVERT: H 116 THR cc_start: 0.7542 (m) cc_final: 0.7069 (p) REVERT: H 117 LEU cc_start: 0.8307 (tp) cc_final: 0.8021 (tp) REVERT: H 172 THR cc_start: 0.8497 (m) cc_final: 0.7927 (p) REVERT: H 176 VAL cc_start: 0.7895 (t) cc_final: 0.7490 (p) REVERT: H 189 VAL cc_start: 0.8611 (t) cc_final: 0.8213 (p) REVERT: H 200 THR cc_start: 0.8574 (m) cc_final: 0.8243 (t) REVERT: H 201 TYR cc_start: 0.6285 (m-80) cc_final: 0.6035 (m-80) REVERT: L 35 TRP cc_start: 0.6206 (OUTLIER) cc_final: 0.5637 (m-90) REVERT: L 83 PHE cc_start: 0.7358 (m-80) cc_final: 0.7072 (m-80) REVERT: L 97 MET cc_start: 0.6328 (mtm) cc_final: 0.5999 (mtm) REVERT: L 164 SER cc_start: 0.8467 (t) cc_final: 0.8112 (p) REVERT: L 178 SER cc_start: 0.8327 (t) cc_final: 0.7557 (m) REVERT: A 269 TYR cc_start: 0.7768 (m-80) cc_final: 0.7514 (m-80) REVERT: A 298 GLU cc_start: 0.7478 (tt0) cc_final: 0.7191 (tt0) REVERT: A 345 THR cc_start: 0.7192 (p) cc_final: 0.6894 (t) REVERT: A 353 TRP cc_start: 0.8092 (p-90) cc_final: 0.7532 (p-90) REVERT: A 382 VAL cc_start: 0.6118 (OUTLIER) cc_final: 0.5232 (p) REVERT: A 392 PHE cc_start: 0.7399 (m-10) cc_final: 0.7109 (m-10) REVERT: A 406 GLU cc_start: 0.7469 (pt0) cc_final: 0.7217 (pt0) REVERT: A 424 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7491 (ttmm) REVERT: A 436 TRP cc_start: 0.7361 (p90) cc_final: 0.6745 (p90) REVERT: A 448 ASN cc_start: 0.7153 (m-40) cc_final: 0.6929 (m-40) REVERT: A 460 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7782 (mptm) REVERT: A 465 GLU cc_start: 0.6916 (tt0) cc_final: 0.6336 (tt0) REVERT: A 493 GLN cc_start: 0.6394 (tp40) cc_final: 0.5924 (tp40) REVERT: A 510 VAL cc_start: 0.8380 (OUTLIER) cc_final: 0.7932 (m) REVERT: A 511 VAL cc_start: 0.7847 (OUTLIER) cc_final: 0.7561 (p) REVERT: A 528 LYS cc_start: 0.4746 (OUTLIER) cc_final: 0.4511 (mmmt) REVERT: A 539 VAL cc_start: 0.7775 (t) cc_final: 0.7561 (p) REVERT: A 592 PHE cc_start: 0.1846 (OUTLIER) cc_final: -0.0143 (m-10) REVERT: A 697 MET cc_start: -0.4626 (ptp) cc_final: -0.5443 (ptt) outliers start: 54 outliers final: 35 residues processed: 238 average time/residue: 0.2223 time to fit residues: 71.4112 Evaluate side-chains 245 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 202 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 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 58 ILE 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 L residue 177 LEU Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain L residue 211 PHE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 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 358 ILE 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 395 VAL Chi-restraints excluded: chain A residue 424 LYS 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 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 596 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 171 HIS L 90 HIS L 149 GLN L 168 GLN A 422 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5998 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 8588 Z= 0.300 Angle : 0.675 9.405 11689 Z= 0.343 Chirality : 0.048 0.291 1302 Planarity : 0.005 0.059 1507 Dihedral : 7.315 87.496 1201 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.52 % Favored : 89.48 % Rotamer: Outliers : 5.43 % Allowed : 17.36 % Favored : 77.21 % 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: -2.68 (0.24), residues: 1065 helix: -1.55 (0.83), residues: 32 sheet: -1.01 (0.30), residues: 313 loop : -2.30 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 150 HIS 0.005 0.001 HIS L 191 PHE 0.025 0.002 PHE A 377 TYR 0.019 0.002 TYR A 265 ARG 0.003 0.001 ARG A 403 *********************** 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 273 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 222 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLN cc_start: 0.6857 (tt0) cc_final: 0.6499 (tt0) REVERT: H 29 PHE cc_start: 0.7963 (t80) cc_final: 0.7720 (t80) REVERT: H 85 SER cc_start: 0.7467 (t) cc_final: 0.7000 (p) REVERT: H 116 THR cc_start: 0.7603 (m) cc_final: 0.7232 (p) REVERT: H 117 LEU cc_start: 0.8390 (tp) cc_final: 0.8050 (tp) REVERT: H 176 VAL cc_start: 0.7959 (t) cc_final: 0.7565 (p) REVERT: H 187 SER cc_start: 0.8409 (t) cc_final: 0.8081 (p) REVERT: H 189 VAL cc_start: 0.8874 (t) cc_final: 0.8403 (p) REVERT: H 200 THR cc_start: 0.8711 (m) cc_final: 0.8397 (t) REVERT: L 4 LEU cc_start: 0.7557 (mt) cc_final: 0.7233 (tp) REVERT: L 29 VAL cc_start: 0.7225 (m) cc_final: 0.7023 (m) REVERT: L 61 ARG cc_start: 0.7613 (ptt-90) cc_final: 0.7250 (ptt-90) REVERT: L 83 PHE cc_start: 0.7413 (m-80) cc_final: 0.7096 (m-80) REVERT: L 97 MET cc_start: 0.6377 (mtm) cc_final: 0.5937 (mtm) REVERT: L 107 GLU cc_start: 0.6788 (mm-30) cc_final: 0.6453 (mm-30) REVERT: L 164 SER cc_start: 0.8499 (t) cc_final: 0.8128 (p) REVERT: L 178 SER cc_start: 0.8389 (t) cc_final: 0.7557 (m) REVERT: A 126 ASN cc_start: 0.5911 (p0) cc_final: 0.5666 (p0) REVERT: A 298 GLU cc_start: 0.7662 (tt0) cc_final: 0.7253 (tt0) REVERT: A 345 THR cc_start: 0.7247 (p) cc_final: 0.7045 (t) REVERT: A 353 TRP cc_start: 0.8187 (p-90) cc_final: 0.7581 (p-90) REVERT: A 357 ARG cc_start: 0.7712 (ptm-80) cc_final: 0.7178 (ptm-80) REVERT: A 375 PHE cc_start: 0.8290 (t80) cc_final: 0.7919 (t80) REVERT: A 382 VAL cc_start: 0.6341 (OUTLIER) cc_final: 0.5483 (p) REVERT: A 394 ASN cc_start: 0.7016 (t0) cc_final: 0.6589 (t0) REVERT: A 406 GLU cc_start: 0.7443 (pt0) cc_final: 0.7148 (pt0) REVERT: A 424 LYS cc_start: 0.7912 (ttmm) cc_final: 0.7705 (ttmm) REVERT: A 436 TRP cc_start: 0.7582 (p90) cc_final: 0.6861 (p90) REVERT: A 448 ASN cc_start: 0.7176 (m-40) cc_final: 0.6890 (m-40) REVERT: A 460 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7800 (mptm) REVERT: A 465 GLU cc_start: 0.6932 (tt0) cc_final: 0.6370 (tt0) REVERT: A 510 VAL cc_start: 0.8389 (p) cc_final: 0.7922 (m) REVERT: A 515 PHE cc_start: 0.7670 (m-10) cc_final: 0.7339 (m-10) REVERT: A 592 PHE cc_start: 0.2563 (OUTLIER) cc_final: -0.0290 (m-80) outliers start: 51 outliers final: 37 residues processed: 245 average time/residue: 0.2150 time to fit residues: 71.1560 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 : 0.868 ------------------------------------------------------------------------------- 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 69 THR Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain L residue 211 PHE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 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 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 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 596 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 64 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 80 optimal weight: 0.0870 chunk 92 optimal weight: 0.0370 chunk 97 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 171 HIS A 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5922 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8588 Z= 0.179 Angle : 0.618 8.153 11689 Z= 0.309 Chirality : 0.045 0.161 1302 Planarity : 0.004 0.061 1507 Dihedral : 6.958 87.151 1198 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 4.69 % Allowed : 18.85 % 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: -2.56 (0.25), residues: 1065 helix: -1.49 (0.85), residues: 32 sheet: -0.94 (0.30), residues: 313 loop : -2.20 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 150 HIS 0.001 0.000 HIS A 67 PHE 0.019 0.002 PHE H 29 TYR 0.013 0.001 TYR H 60 ARG 0.002 0.000 ARG A 246 *********************** 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 257 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 213 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.7759 (mp) cc_final: 0.7273 (tt) REVERT: H 6 GLN cc_start: 0.6720 (tt0) cc_final: 0.6399 (tt0) REVERT: H 22 CYS cc_start: 0.5730 (t) cc_final: 0.4175 (t) REVERT: H 29 PHE cc_start: 0.7831 (t80) cc_final: 0.7625 (t80) REVERT: H 83 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8340 (tp) REVERT: H 85 SER cc_start: 0.7425 (t) cc_final: 0.6964 (p) REVERT: H 116 THR cc_start: 0.7533 (m) cc_final: 0.7095 (p) REVERT: H 117 LEU cc_start: 0.8331 (tp) cc_final: 0.8020 (tp) REVERT: H 172 THR cc_start: 0.8431 (m) cc_final: 0.7859 (p) REVERT: H 176 VAL cc_start: 0.7900 (t) cc_final: 0.7539 (p) REVERT: H 189 VAL cc_start: 0.8728 (t) cc_final: 0.8309 (p) REVERT: H 200 THR cc_start: 0.8690 (m) cc_final: 0.8380 (t) REVERT: L 4 LEU cc_start: 0.7446 (mt) cc_final: 0.6896 (tp) REVERT: L 35 TRP cc_start: 0.6185 (OUTLIER) cc_final: 0.5391 (m-90) REVERT: L 83 PHE cc_start: 0.7301 (m-80) cc_final: 0.7051 (m-80) REVERT: L 107 GLU cc_start: 0.6831 (mm-30) cc_final: 0.6472 (mm-30) REVERT: L 164 SER cc_start: 0.8573 (t) cc_final: 0.8189 (p) REVERT: L 169 ASP cc_start: 0.7913 (t0) cc_final: 0.7370 (p0) REVERT: L 178 SER cc_start: 0.8304 (t) cc_final: 0.7535 (m) REVERT: A 269 TYR cc_start: 0.7913 (m-80) cc_final: 0.7698 (m-80) REVERT: A 353 TRP cc_start: 0.8100 (p-90) cc_final: 0.7574 (p-90) REVERT: A 357 ARG cc_start: 0.7733 (ptm-80) cc_final: 0.6958 (ptm-80) REVERT: A 382 VAL cc_start: 0.6281 (OUTLIER) cc_final: 0.5389 (p) REVERT: A 394 ASN cc_start: 0.6787 (t0) cc_final: 0.6303 (t0) REVERT: A 406 GLU cc_start: 0.7473 (pt0) cc_final: 0.7171 (pt0) REVERT: A 424 LYS cc_start: 0.7660 (ttmm) cc_final: 0.7308 (ttmm) REVERT: A 433 VAL cc_start: 0.7799 (p) cc_final: 0.7353 (m) REVERT: A 436 TRP cc_start: 0.7459 (p90) cc_final: 0.6845 (p90) REVERT: A 448 ASN cc_start: 0.7139 (m-40) cc_final: 0.6836 (m-40) REVERT: A 460 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7746 (mptm) REVERT: A 465 GLU cc_start: 0.6941 (tt0) cc_final: 0.6363 (tt0) REVERT: A 510 VAL cc_start: 0.8357 (p) cc_final: 0.7878 (m) REVERT: A 511 VAL cc_start: 0.7763 (OUTLIER) cc_final: 0.7406 (p) REVERT: A 515 PHE cc_start: 0.7619 (m-10) cc_final: 0.7355 (m-10) REVERT: A 531 THR cc_start: 0.6627 (OUTLIER) cc_final: 0.6122 (p) REVERT: A 592 PHE cc_start: 0.2200 (OUTLIER) cc_final: -0.0520 (m-10) REVERT: A 697 MET cc_start: -0.4014 (mtt) cc_final: -0.5481 (ptt) outliers start: 44 outliers final: 32 residues processed: 235 average time/residue: 0.2202 time to fit residues: 69.5017 Evaluate side-chains 246 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 207 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 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 69 THR Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 182 THR 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 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 390 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL 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 531 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 596 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 32 HIS H 107 ASN H 171 HIS A 422 ASN A 474 GLN A 677 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6083 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.163 8588 Z= 0.418 Angle : 0.757 10.658 11689 Z= 0.392 Chirality : 0.049 0.173 1302 Planarity : 0.005 0.065 1507 Dihedral : 7.599 87.205 1198 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.21 % Favored : 87.79 % Rotamer: Outliers : 5.43 % Allowed : 18.32 % Favored : 76.25 % 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: -2.82 (0.24), residues: 1065 helix: -2.00 (0.72), residues: 31 sheet: -1.01 (0.30), residues: 300 loop : -2.41 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP L 150 HIS 0.008 0.002 HIS A 245 PHE 0.025 0.003 PHE A 377 TYR 0.025 0.003 TYR L 175 ARG 0.003 0.001 ARG H 38 *********************** 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 270 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 219 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.7880 (mp) cc_final: 0.7408 (tt) REVERT: H 6 GLN cc_start: 0.6904 (tt0) cc_final: 0.6598 (tt0) REVERT: H 29 PHE cc_start: 0.8045 (t80) cc_final: 0.7822 (t80) REVERT: H 65 GLN cc_start: 0.7373 (tt0) cc_final: 0.7140 (tt0) REVERT: H 83 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8475 (tp) REVERT: H 85 SER cc_start: 0.7676 (t) cc_final: 0.7199 (p) REVERT: H 116 THR cc_start: 0.7700 (m) cc_final: 0.7332 (p) REVERT: H 117 LEU cc_start: 0.8393 (tp) cc_final: 0.8092 (tp) REVERT: H 172 THR cc_start: 0.8487 (m) cc_final: 0.7951 (p) REVERT: H 176 VAL cc_start: 0.8034 (t) cc_final: 0.7668 (p) REVERT: H 187 SER cc_start: 0.8510 (t) cc_final: 0.8189 (p) REVERT: H 200 THR cc_start: 0.8751 (m) cc_final: 0.8454 (t) REVERT: L 4 LEU cc_start: 0.7680 (mt) cc_final: 0.7369 (tp) REVERT: L 58 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8331 (tt) REVERT: L 83 PHE cc_start: 0.7470 (m-80) cc_final: 0.7147 (m-80) REVERT: L 107 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6627 (mm-30) REVERT: L 164 SER cc_start: 0.8477 (t) cc_final: 0.8099 (p) REVERT: L 178 SER cc_start: 0.8402 (t) cc_final: 0.7586 (m) REVERT: A 126 ASN cc_start: 0.5824 (p0) cc_final: 0.5531 (p0) REVERT: A 269 TYR cc_start: 0.7943 (m-80) cc_final: 0.7710 (m-80) REVERT: A 298 GLU cc_start: 0.7727 (tt0) cc_final: 0.7245 (tt0) REVERT: A 345 THR cc_start: 0.7350 (p) cc_final: 0.7098 (t) REVERT: A 394 ASN cc_start: 0.7057 (t0) cc_final: 0.6824 (t0) REVERT: A 406 GLU cc_start: 0.7406 (pt0) cc_final: 0.6239 (pt0) REVERT: A 409 GLN cc_start: 0.7833 (mt0) cc_final: 0.7541 (mt0) REVERT: A 424 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7731 (ttmm) REVERT: A 448 ASN cc_start: 0.7421 (m-40) cc_final: 0.7152 (m-40) REVERT: A 460 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7814 (mptm) REVERT: A 465 GLU cc_start: 0.6985 (tt0) cc_final: 0.6391 (tt0) REVERT: A 510 VAL cc_start: 0.8402 (OUTLIER) cc_final: 0.7984 (m) REVERT: A 531 THR cc_start: 0.6988 (OUTLIER) cc_final: 0.6473 (m) REVERT: A 592 PHE cc_start: 0.3621 (OUTLIER) cc_final: 0.0286 (m-10) outliers start: 51 outliers final: 38 residues processed: 245 average time/residue: 0.2177 time to fit residues: 72.0788 Evaluate side-chains 261 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 216 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 83 LEU 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 69 THR Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain L residue 201 GLN Chi-restraints excluded: chain L residue 211 PHE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 677 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 107 ASN H 171 HIS L 102 GLN A 122 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6095 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.131 8588 Z= 0.381 Angle : 0.754 11.298 11689 Z= 0.391 Chirality : 0.050 0.203 1302 Planarity : 0.005 0.064 1507 Dihedral : 7.550 86.796 1193 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 4.90 % Allowed : 19.17 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.24), residues: 1065 helix: -2.40 (0.72), residues: 31 sheet: -1.13 (0.29), residues: 306 loop : -2.55 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP A 105 HIS 0.006 0.002 HIS A 245 PHE 0.024 0.003 PHE A 377 TYR 0.030 0.002 TYR A 423 ARG 0.006 0.001 ARG A 328 ********************** 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 258 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 212 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.7879 (mp) cc_final: 0.7444 (tt) REVERT: H 6 GLN cc_start: 0.6924 (tt0) cc_final: 0.6609 (tt0) REVERT: H 29 PHE cc_start: 0.7999 (t80) cc_final: 0.7787 (t80) REVERT: H 63 LYS cc_start: 0.8563 (tmtt) cc_final: 0.8291 (tmtt) REVERT: H 65 GLN cc_start: 0.7316 (tt0) cc_final: 0.7088 (tt0) REVERT: H 83 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8448 (tp) REVERT: H 85 SER cc_start: 0.7764 (t) cc_final: 0.7279 (p) REVERT: H 116 THR cc_start: 0.7669 (m) cc_final: 0.7375 (p) REVERT: H 117 LEU cc_start: 0.8409 (tp) cc_final: 0.8117 (tp) REVERT: H 172 THR cc_start: 0.8485 (m) cc_final: 0.7967 (p) REVERT: H 176 VAL cc_start: 0.8029 (t) cc_final: 0.7678 (p) REVERT: H 187 SER cc_start: 0.8479 (t) cc_final: 0.8143 (p) REVERT: H 200 THR cc_start: 0.8786 (m) cc_final: 0.8526 (t) REVERT: L 4 LEU cc_start: 0.7637 (mt) cc_final: 0.7256 (tp) REVERT: L 58 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8382 (tt) REVERT: L 83 PHE cc_start: 0.7486 (m-80) cc_final: 0.7141 (m-80) REVERT: L 107 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6598 (mm-30) REVERT: L 164 SER cc_start: 0.8489 (t) cc_final: 0.8137 (p) REVERT: L 178 SER cc_start: 0.8372 (t) cc_final: 0.7560 (m) REVERT: A 126 ASN cc_start: 0.5550 (p0) cc_final: 0.5280 (p0) REVERT: A 269 TYR cc_start: 0.8014 (m-80) cc_final: 0.7741 (m-80) REVERT: A 298 GLU cc_start: 0.7709 (tt0) cc_final: 0.7113 (tt0) REVERT: A 331 ASN cc_start: 0.7347 (t0) cc_final: 0.7132 (t0) REVERT: A 406 GLU cc_start: 0.7439 (pt0) cc_final: 0.7186 (pt0) REVERT: A 424 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7580 (ttmm) REVERT: A 448 ASN cc_start: 0.7449 (m-40) cc_final: 0.7203 (m-40) REVERT: A 460 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7745 (mptm) REVERT: A 465 GLU cc_start: 0.6979 (tt0) cc_final: 0.6525 (tt0) REVERT: A 510 VAL cc_start: 0.8430 (p) cc_final: 0.8010 (m) REVERT: A 531 THR cc_start: 0.7068 (OUTLIER) cc_final: 0.6450 (p) REVERT: A 592 PHE cc_start: 0.3565 (OUTLIER) cc_final: 0.0123 (m-10) outliers start: 46 outliers final: 35 residues processed: 236 average time/residue: 0.2176 time to fit residues: 69.9908 Evaluate side-chains 257 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 216 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 83 LEU 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 58 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 177 LEU Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain L residue 211 PHE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 424 LYS 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 531 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 596 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 chunk 73 optimal weight: 0.0370 chunk 4 optimal weight: 0.4980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 171 HIS H 206 ASN A 422 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.210300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.177445 restraints weight = 17625.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.182806 restraints weight = 9462.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.186223 restraints weight = 5769.241| |-----------------------------------------------------------------------------| r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5980 moved from start: 0.5576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8588 Z= 0.188 Angle : 0.660 9.501 11689 Z= 0.333 Chirality : 0.046 0.163 1302 Planarity : 0.005 0.109 1507 Dihedral : 7.114 86.750 1193 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 4.05 % Allowed : 20.34 % Favored : 75.61 % 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: -2.71 (0.25), residues: 1065 helix: -2.12 (0.80), residues: 32 sheet: -1.01 (0.30), residues: 317 loop : -2.30 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 105 HIS 0.003 0.001 HIS A 67 PHE 0.019 0.002 PHE L 118 TYR 0.016 0.001 TYR H 152 ARG 0.003 0.000 ARG L 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2315.00 seconds wall clock time: 42 minutes 31.22 seconds (2551.22 seconds total)