Starting phenix.real_space_refine on Wed Feb 12 03:07:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vk1_21223/02_2025/6vk1_21223.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vk1_21223/02_2025/6vk1_21223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vk1_21223/02_2025/6vk1_21223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vk1_21223/02_2025/6vk1_21223.map" model { file = "/net/cci-nas-00/data/ceres_data/6vk1_21223/02_2025/6vk1_21223.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vk1_21223/02_2025/6vk1_21223.cif" } resolution = 3.9 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= -0.000 sd= 0.008 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 34 5.16 5 C 4712 2.51 5 N 1203 2.21 5 O 1310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7259 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2343 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 4916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4916 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 20, 'TRANS': 581} Chain breaks: 5 Time building chain proxies: 4.15, per 1000 atoms: 0.57 Number of scatterers: 7259 At special positions: 0 Unit cell: (78.3, 99.9, 152.55, 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 34 16.00 O 1310 8.00 N 1203 7.00 C 4712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.62 Conformation dependent library (CDL) restraints added in 896.7 milliseconds 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1700 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 0 sheets defined 79.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'B' and resid 3 through 31 Processing helix chain 'B' and resid 34 through 43 Processing helix chain 'B' and resid 44 through 71 Processing helix chain 'B' and resid 75 through 98 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 99 through 100 No H-bonds generated for 'chain 'B' and resid 99 through 100' Processing helix chain 'B' and resid 101 through 104 Processing helix chain 'B' and resid 105 through 135 removed outlier: 3.856A pdb=" N ALA B 109 " --> pdb=" O PHE B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 175 Processing helix chain 'B' and resid 179 through 220 removed outlier: 3.560A pdb=" N THR B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 294 removed outlier: 4.022A pdb=" N TYR B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) Proline residue: B 292 - end of helix Processing helix chain 'B' and resid 297 through 324 Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 42 through 47 Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 83 through 100 removed outlier: 3.583A pdb=" N PHE A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.877A pdb=" N THR A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 138 Processing helix chain 'A' and resid 142 through 156 removed outlier: 3.676A pdb=" N ILE A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 184 removed outlier: 3.604A pdb=" N ALA A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 200 removed outlier: 3.601A pdb=" N LYS A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 224 removed outlier: 4.131A pdb=" N SER A 210 " --> pdb=" O ASN A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 removed outlier: 3.630A pdb=" N TRP A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 4.318A pdb=" N ILE A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 355 removed outlier: 3.932A pdb=" N ALA A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 361 removed outlier: 5.558A pdb=" N ASP A 359 " --> pdb=" O PRO A 356 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN A 360 " --> pdb=" O HIS A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 383 removed outlier: 4.058A pdb=" N TYR A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 407 removed outlier: 3.931A pdb=" N ARG A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 426 removed outlier: 3.869A pdb=" N TYR A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 441 removed outlier: 3.995A pdb=" N ALA A 433 " --> pdb=" O ASN A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 461 Processing helix chain 'A' and resid 462 through 465 removed outlier: 4.080A pdb=" N LYS A 465 " --> pdb=" O PRO A 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 465' Processing helix chain 'A' and resid 468 through 480 Processing helix chain 'A' and resid 481 through 495 removed outlier: 3.708A pdb=" N TYR A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 517 removed outlier: 3.767A pdb=" N THR A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU A 517 " --> pdb=" O VAL A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 532 removed outlier: 3.911A pdb=" N THR A 526 " --> pdb=" O PRO A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 548 removed outlier: 4.023A pdb=" N ALA A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU A 548 " --> pdb=" O SER A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 563 Processing helix chain 'A' and resid 576 through 594 removed outlier: 3.805A pdb=" N SER A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY A 594 " --> pdb=" O ALA A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 609 removed outlier: 3.683A pdb=" N VAL A 600 " --> pdb=" O ILE A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 624 removed outlier: 3.662A pdb=" N LEU A 618 " --> pdb=" O LYS A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 647 through 662 removed outlier: 3.686A pdb=" N ASP A 662 " --> pdb=" O VAL A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 682 498 hydrogen bonds defined for protein. 1488 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: 2.01 Time building geometry restraints manager: 1.87 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: 2267 1.34 - 1.46: 1464 1.46 - 1.58: 3645 1.58 - 1.69: 0 1.69 - 1.81: 61 Bond restraints: 7437 Sorted by residual: bond pdb=" N HIS B 101 " pdb=" CA HIS B 101 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.91e+00 bond pdb=" N GLU B 102 " pdb=" CA GLU B 102 " ideal model delta sigma weight residual 1.458 1.490 -0.031 1.27e-02 6.20e+03 6.07e+00 bond pdb=" N ARG B 103 " pdb=" CA ARG B 103 " ideal model delta sigma weight residual 1.459 1.486 -0.028 1.16e-02 7.43e+03 5.72e+00 bond pdb=" CE1 HIS B 101 " pdb=" NE2 HIS B 101 " ideal model delta sigma weight residual 1.321 1.338 -0.017 1.00e-02 1.00e+04 3.03e+00 bond pdb=" CA HIS B 101 " pdb=" C HIS B 101 " ideal model delta sigma weight residual 1.523 1.538 -0.015 1.34e-02 5.57e+03 1.30e+00 ... (remaining 7432 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 9622 1.28 - 2.57: 370 2.57 - 3.85: 56 3.85 - 5.14: 13 5.14 - 6.42: 4 Bond angle restraints: 10065 Sorted by residual: angle pdb=" N GLY A 253 " pdb=" CA GLY A 253 " pdb=" C GLY A 253 " ideal model delta sigma weight residual 112.48 118.47 -5.99 1.21e+00 6.83e-01 2.45e+01 angle pdb=" C ASN A 533 " pdb=" N ASP A 534 " pdb=" CA ASP A 534 " ideal model delta sigma weight residual 121.54 127.96 -6.42 1.91e+00 2.74e-01 1.13e+01 angle pdb=" C PHE A 201 " pdb=" N ASN A 202 " pdb=" CA ASN A 202 " ideal model delta sigma weight residual 121.54 127.39 -5.85 1.91e+00 2.74e-01 9.38e+00 angle pdb=" CA ARG B 103 " pdb=" C ARG B 103 " pdb=" O ARG B 103 " ideal model delta sigma weight residual 121.07 117.91 3.16 1.10e+00 8.26e-01 8.26e+00 angle pdb=" C PHE B 214 " pdb=" N TYR B 215 " pdb=" CA TYR B 215 " ideal model delta sigma weight residual 120.79 124.54 -3.75 1.39e+00 5.18e-01 7.29e+00 ... (remaining 10060 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 3880 17.65 - 35.31: 440 35.31 - 52.96: 64 52.96 - 70.61: 14 70.61 - 88.26: 5 Dihedral angle restraints: 4403 sinusoidal: 1772 harmonic: 2631 Sorted by residual: dihedral pdb=" CA ASN A 645 " pdb=" C ASN A 645 " pdb=" N ARG A 646 " pdb=" CA ARG A 646 " ideal model delta harmonic sigma weight residual 180.00 157.61 22.39 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA ALA A 38 " pdb=" C ALA A 38 " pdb=" N LYS A 39 " pdb=" CA LYS A 39 " ideal model delta harmonic sigma weight residual -180.00 -160.05 -19.95 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA SER A 245 " pdb=" C SER A 245 " pdb=" N ASP A 246 " pdb=" CA ASP A 246 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 4400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 784 0.037 - 0.075: 265 0.075 - 0.112: 46 0.112 - 0.149: 10 0.149 - 0.187: 1 Chirality restraints: 1106 Sorted by residual: chirality pdb=" CA LEU A 252 " pdb=" N LEU A 252 " pdb=" C LEU A 252 " pdb=" CB LEU A 252 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" CB VAL B 155 " pdb=" CA VAL B 155 " pdb=" CG1 VAL B 155 " pdb=" CG2 VAL B 155 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA VAL A 203 " pdb=" N VAL A 203 " pdb=" C VAL A 203 " pdb=" CB VAL A 203 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 1103 not shown) Planarity restraints: 1257 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 295 " -0.029 5.00e-02 4.00e+02 4.33e-02 3.01e+00 pdb=" N PRO B 296 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 296 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 296 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 2 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO B 3 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 3 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 3 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 102 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" C GLU B 102 " 0.027 2.00e-02 2.50e+03 pdb=" O GLU B 102 " -0.010 2.00e-02 2.50e+03 pdb=" N ARG B 103 " -0.009 2.00e-02 2.50e+03 ... (remaining 1254 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1500 2.78 - 3.31: 7437 3.31 - 3.84: 11683 3.84 - 4.37: 12815 4.37 - 4.90: 21844 Nonbonded interactions: 55279 Sorted by model distance: nonbonded pdb=" O THR B 144 " pdb=" OG SER B 148 " model vdw 2.245 3.040 nonbonded pdb=" CD1 LEU B 285 " pdb=" ND1 HIS B 286 " model vdw 2.250 3.540 nonbonded pdb=" O ASP B 179 " pdb=" OG SER B 182 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR A 425 " pdb=" OE1 GLN A 453 " model vdw 2.293 3.040 nonbonded pdb=" OH TYR B 104 " pdb=" OD2 ASP B 179 " model vdw 2.296 3.040 ... (remaining 55274 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.160 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: 0.210 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 18.610 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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 0.036 7437 Z= 0.174 Angle : 0.590 6.422 10065 Z= 0.362 Chirality : 0.038 0.187 1106 Planarity : 0.004 0.043 1257 Dihedral : 14.769 88.262 2703 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.13 % Allowed : 5.08 % Favored : 94.80 % 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: -1.86 (0.25), residues: 866 helix: -0.46 (0.18), residues: 659 sheet: None (None), residues: 0 loop : -3.52 (0.32), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 27 HIS 0.004 0.001 HIS A 143 PHE 0.013 0.001 PHE B 147 TYR 0.011 0.001 TYR A 74 ARG 0.003 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 GLN cc_start: 0.8411 (mt0) cc_final: 0.8099 (tm-30) REVERT: B 60 THR cc_start: 0.9237 (p) cc_final: 0.8945 (p) REVERT: B 85 ARG cc_start: 0.8645 (mmt180) cc_final: 0.7809 (mmm160) REVERT: B 103 ARG cc_start: 0.5868 (mpp80) cc_final: 0.4330 (ptm-80) REVERT: B 118 LEU cc_start: 0.8831 (mt) cc_final: 0.8259 (mt) REVERT: B 119 LYS cc_start: 0.9163 (mtmt) cc_final: 0.8932 (mtpp) REVERT: B 122 HIS cc_start: 0.8242 (m90) cc_final: 0.7997 (m170) REVERT: B 124 ILE cc_start: 0.9062 (pt) cc_final: 0.8740 (pt) REVERT: B 197 LEU cc_start: 0.9220 (tp) cc_final: 0.8927 (tp) REVERT: B 202 ASN cc_start: 0.7890 (t0) cc_final: 0.7326 (t0) REVERT: B 206 GLN cc_start: 0.7832 (mt0) cc_final: 0.7278 (mt0) REVERT: A 149 LEU cc_start: 0.9375 (tp) cc_final: 0.9067 (mm) REVERT: A 238 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7682 (mt-10) REVERT: A 416 CYS cc_start: 0.8270 (m) cc_final: 0.8053 (m) REVERT: A 639 GLU cc_start: 0.8036 (pp20) cc_final: 0.7656 (pt0) REVERT: A 642 LEU cc_start: 0.6236 (pp) cc_final: 0.5211 (pp) REVERT: A 676 LEU cc_start: 0.7656 (tp) cc_final: 0.7311 (tp) outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.2202 time to fit residues: 67.9895 Evaluate side-chains 169 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 HIS B 189 GLN A 86 GLN A 101 ASN A 113 HIS A 202 ASN A 593 GLN A 620 GLN ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.153028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.121589 restraints weight = 12494.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.118958 restraints weight = 10594.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.120370 restraints weight = 10923.193| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7437 Z= 0.251 Angle : 0.632 13.576 10065 Z= 0.330 Chirality : 0.041 0.201 1106 Planarity : 0.004 0.045 1257 Dihedral : 4.557 21.691 973 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.28 % Allowed : 14.72 % Favored : 82.99 % 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: 0.06 (0.27), residues: 866 helix: 0.96 (0.19), residues: 663 sheet: None (None), residues: 0 loop : -3.11 (0.34), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 27 HIS 0.009 0.001 HIS B 122 PHE 0.019 0.002 PHE B 293 TYR 0.017 0.002 TYR A 486 ARG 0.003 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 GLN cc_start: 0.8679 (mt0) cc_final: 0.8230 (tm-30) REVERT: B 60 THR cc_start: 0.9235 (p) cc_final: 0.8978 (p) REVERT: B 83 PHE cc_start: 0.6903 (t80) cc_final: 0.6625 (t80) REVERT: B 85 ARG cc_start: 0.8980 (mmt180) cc_final: 0.7761 (mmm160) REVERT: B 103 ARG cc_start: 0.6119 (mpp80) cc_final: 0.4011 (ttp-170) REVERT: B 118 LEU cc_start: 0.8864 (mt) cc_final: 0.8603 (mm) REVERT: B 128 ARG cc_start: 0.7905 (mmm160) cc_final: 0.7668 (mmm160) REVERT: B 189 GLN cc_start: 0.8970 (mp10) cc_final: 0.8624 (mp10) REVERT: B 197 LEU cc_start: 0.9373 (tp) cc_final: 0.8945 (tp) REVERT: B 298 MET cc_start: 0.8301 (mtt) cc_final: 0.7839 (mtm) REVERT: A 74 TYR cc_start: 0.7458 (t80) cc_final: 0.7129 (t80) REVERT: A 149 LEU cc_start: 0.9315 (tp) cc_final: 0.9076 (mm) REVERT: A 416 CYS cc_start: 0.8467 (m) cc_final: 0.8108 (m) REVERT: A 423 ASN cc_start: 0.8457 (p0) cc_final: 0.8245 (p0) REVERT: A 656 ASP cc_start: 0.7684 (m-30) cc_final: 0.7408 (m-30) outliers start: 18 outliers final: 8 residues processed: 182 average time/residue: 0.1838 time to fit residues: 45.0538 Evaluate side-chains 172 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 631 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 27 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 46 optimal weight: 0.2980 chunk 26 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.153079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.122436 restraints weight = 12742.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.119825 restraints weight = 11177.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.121201 restraints weight = 11645.440| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7437 Z= 0.218 Angle : 0.602 11.886 10065 Z= 0.313 Chirality : 0.039 0.125 1106 Planarity : 0.004 0.051 1257 Dihedral : 4.435 20.781 973 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.41 % Allowed : 17.89 % Favored : 79.70 % 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: 0.85 (0.28), residues: 866 helix: 1.52 (0.19), residues: 662 sheet: None (None), residues: 0 loop : -2.73 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 632 HIS 0.005 0.001 HIS B 79 PHE 0.026 0.002 PHE B 293 TYR 0.013 0.001 TYR A 486 ARG 0.004 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 9 GLN cc_start: 0.8672 (mt0) cc_final: 0.8177 (tm-30) REVERT: B 60 THR cc_start: 0.9144 (p) cc_final: 0.8892 (p) REVERT: B 83 PHE cc_start: 0.6805 (t80) cc_final: 0.6548 (t80) REVERT: B 85 ARG cc_start: 0.8840 (mmt180) cc_final: 0.7702 (mmm160) REVERT: B 103 ARG cc_start: 0.6059 (mpp80) cc_final: 0.3676 (ttp-170) REVERT: B 128 ARG cc_start: 0.7771 (mmm160) cc_final: 0.7559 (mmm160) REVERT: B 189 GLN cc_start: 0.8918 (mp10) cc_final: 0.8673 (mp10) REVERT: B 195 MET cc_start: 0.8155 (mtp) cc_final: 0.7693 (mtp) REVERT: B 197 LEU cc_start: 0.9373 (tp) cc_final: 0.8951 (tp) REVERT: B 271 GLU cc_start: 0.7817 (pt0) cc_final: 0.7089 (pt0) REVERT: B 272 LYS cc_start: 0.8327 (mptt) cc_final: 0.7860 (mmtm) REVERT: B 298 MET cc_start: 0.8354 (mtt) cc_final: 0.8049 (mtm) REVERT: A 74 TYR cc_start: 0.7598 (t80) cc_final: 0.7208 (t80) REVERT: A 152 MET cc_start: 0.8924 (tpp) cc_final: 0.8439 (tpp) REVERT: A 416 CYS cc_start: 0.8472 (m) cc_final: 0.8123 (m) REVERT: A 423 ASN cc_start: 0.8425 (p0) cc_final: 0.8163 (p0) REVERT: A 620 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.7149 (tm130) REVERT: A 656 ASP cc_start: 0.7740 (m-30) cc_final: 0.7467 (m-30) outliers start: 19 outliers final: 7 residues processed: 182 average time/residue: 0.1814 time to fit residues: 44.6293 Evaluate side-chains 170 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 620 GLN Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 639 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 77 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 32 optimal weight: 0.0040 chunk 27 optimal weight: 9.9990 chunk 78 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.156121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.125357 restraints weight = 12748.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.123242 restraints weight = 10484.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.124277 restraints weight = 11582.527| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7437 Z= 0.151 Angle : 0.574 11.066 10065 Z= 0.293 Chirality : 0.037 0.204 1106 Planarity : 0.003 0.047 1257 Dihedral : 4.253 28.072 973 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.41 % Allowed : 18.65 % Favored : 78.93 % 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: 1.38 (0.28), residues: 866 helix: 1.94 (0.19), residues: 653 sheet: None (None), residues: 0 loop : -2.52 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 78 HIS 0.003 0.001 HIS A 122 PHE 0.035 0.001 PHE B 277 TYR 0.011 0.001 TYR A 436 ARG 0.002 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 GLN cc_start: 0.8624 (mt0) cc_final: 0.8129 (tm-30) REVERT: B 60 THR cc_start: 0.9071 (p) cc_final: 0.8852 (p) REVERT: B 78 GLU cc_start: 0.8409 (pt0) cc_final: 0.8098 (pt0) REVERT: B 83 PHE cc_start: 0.6822 (t80) cc_final: 0.6553 (t80) REVERT: B 85 ARG cc_start: 0.8803 (mmt180) cc_final: 0.7680 (mmm160) REVERT: B 128 ARG cc_start: 0.7676 (mmm160) cc_final: 0.7417 (mmm160) REVERT: B 192 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8040 (mm-30) REVERT: B 195 MET cc_start: 0.8041 (mtp) cc_final: 0.7510 (mtp) REVERT: B 197 LEU cc_start: 0.9350 (tp) cc_final: 0.8950 (tp) REVERT: A 248 GLU cc_start: 0.7334 (mp0) cc_final: 0.7122 (mp0) REVERT: A 344 LYS cc_start: 0.9050 (ttpp) cc_final: 0.8704 (ttpt) REVERT: A 423 ASN cc_start: 0.8320 (p0) cc_final: 0.8035 (p0) REVERT: A 656 ASP cc_start: 0.7518 (m-30) cc_final: 0.7263 (m-30) outliers start: 19 outliers final: 8 residues processed: 193 average time/residue: 0.1721 time to fit residues: 45.5192 Evaluate side-chains 166 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 682 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 64 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 65 optimal weight: 0.4980 chunk 36 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.156839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.125546 restraints weight = 12542.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.124260 restraints weight = 10475.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.125748 restraints weight = 10767.202| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 7437 Z= 0.163 Angle : 0.597 10.533 10065 Z= 0.299 Chirality : 0.038 0.269 1106 Planarity : 0.003 0.048 1257 Dihedral : 4.134 25.305 973 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.66 % Allowed : 20.81 % Favored : 76.52 % 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: 1.64 (0.29), residues: 866 helix: 2.09 (0.19), residues: 656 sheet: None (None), residues: 0 loop : -2.35 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 305 HIS 0.003 0.001 HIS A 122 PHE 0.031 0.001 PHE B 293 TYR 0.016 0.001 TYR A 436 ARG 0.001 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 GLN cc_start: 0.8490 (mt0) cc_final: 0.8021 (tm-30) REVERT: B 78 GLU cc_start: 0.8383 (pt0) cc_final: 0.8065 (pt0) REVERT: B 83 PHE cc_start: 0.6810 (t80) cc_final: 0.6542 (t80) REVERT: B 85 ARG cc_start: 0.8703 (mmt180) cc_final: 0.7691 (mmm160) REVERT: B 191 MET cc_start: 0.7708 (tmm) cc_final: 0.7450 (tmm) REVERT: B 197 LEU cc_start: 0.9268 (tp) cc_final: 0.8804 (tp) REVERT: B 271 GLU cc_start: 0.7695 (pt0) cc_final: 0.7427 (pt0) REVERT: B 272 LYS cc_start: 0.8215 (mptt) cc_final: 0.7968 (mmtm) REVERT: A 248 GLU cc_start: 0.7136 (mp0) cc_final: 0.6933 (mp0) REVERT: A 344 LYS cc_start: 0.9043 (ttpp) cc_final: 0.8708 (ttpt) REVERT: A 419 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8870 (mm) REVERT: A 423 ASN cc_start: 0.8354 (p0) cc_final: 0.8151 (p0) REVERT: A 465 LYS cc_start: 0.7187 (mptt) cc_final: 0.6741 (tptt) REVERT: A 620 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.7157 (tm-30) REVERT: A 656 ASP cc_start: 0.7476 (m-30) cc_final: 0.7183 (m-30) outliers start: 21 outliers final: 12 residues processed: 188 average time/residue: 0.1665 time to fit residues: 43.3683 Evaluate side-chains 173 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 461 PHE Chi-restraints excluded: chain A residue 620 GLN Chi-restraints excluded: chain A residue 633 ASN Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 682 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 87 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 80 optimal weight: 0.0370 chunk 86 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.156983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.124859 restraints weight = 12585.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.123579 restraints weight = 10883.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.125140 restraints weight = 9581.564| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7437 Z= 0.170 Angle : 0.628 10.609 10065 Z= 0.313 Chirality : 0.039 0.303 1106 Planarity : 0.004 0.048 1257 Dihedral : 4.046 24.339 973 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.30 % Allowed : 21.57 % Favored : 75.13 % 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: 1.72 (0.29), residues: 866 helix: 2.16 (0.20), residues: 657 sheet: None (None), residues: 0 loop : -2.35 (0.40), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 305 HIS 0.004 0.001 HIS B 122 PHE 0.048 0.002 PHE B 147 TYR 0.015 0.001 TYR A 436 ARG 0.004 0.000 ARG A 589 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 GLN cc_start: 0.8480 (mt0) cc_final: 0.8101 (tm-30) REVERT: B 78 GLU cc_start: 0.8467 (pt0) cc_final: 0.8180 (pt0) REVERT: B 83 PHE cc_start: 0.6864 (t80) cc_final: 0.6585 (t80) REVERT: B 85 ARG cc_start: 0.8705 (mmt180) cc_final: 0.7671 (mmm160) REVERT: B 191 MET cc_start: 0.7810 (tmm) cc_final: 0.7508 (tmm) REVERT: B 197 LEU cc_start: 0.9296 (tp) cc_final: 0.8924 (tp) REVERT: B 272 LYS cc_start: 0.8217 (mptt) cc_final: 0.8002 (mmtm) REVERT: A 344 LYS cc_start: 0.9005 (ttpp) cc_final: 0.8702 (ttpt) REVERT: A 418 ASP cc_start: 0.8371 (m-30) cc_final: 0.8081 (m-30) REVERT: A 465 LYS cc_start: 0.7176 (mptt) cc_final: 0.6688 (tptt) REVERT: A 656 ASP cc_start: 0.7491 (m-30) cc_final: 0.7203 (m-30) outliers start: 26 outliers final: 17 residues processed: 181 average time/residue: 0.1645 time to fit residues: 41.2270 Evaluate side-chains 175 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 461 PHE Chi-restraints excluded: chain A residue 633 ASN Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 682 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 chunk 3 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 123 ASN A 620 GLN A 633 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.157289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.125792 restraints weight = 12472.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.124771 restraints weight = 10278.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.126141 restraints weight = 10207.960| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7437 Z= 0.179 Angle : 0.660 11.224 10065 Z= 0.333 Chirality : 0.040 0.298 1106 Planarity : 0.004 0.053 1257 Dihedral : 4.037 26.975 973 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.30 % Allowed : 21.57 % Favored : 75.13 % 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: 1.78 (0.29), residues: 866 helix: 2.19 (0.20), residues: 657 sheet: None (None), residues: 0 loop : -2.32 (0.40), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 305 HIS 0.004 0.001 HIS B 122 PHE 0.040 0.001 PHE B 147 TYR 0.015 0.001 TYR A 436 ARG 0.003 0.000 ARG A 589 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3065 (pmm) cc_final: 0.2534 (ptt) REVERT: B 9 GLN cc_start: 0.8433 (mt0) cc_final: 0.8058 (tm-30) REVERT: B 78 GLU cc_start: 0.8341 (pt0) cc_final: 0.8099 (pt0) REVERT: B 83 PHE cc_start: 0.6801 (t80) cc_final: 0.6504 (t80) REVERT: B 85 ARG cc_start: 0.8593 (mmt180) cc_final: 0.7666 (mmm160) REVERT: B 197 LEU cc_start: 0.9275 (tp) cc_final: 0.8804 (tp) REVERT: B 272 LYS cc_start: 0.8274 (mptt) cc_final: 0.7958 (mmtm) REVERT: B 318 TRP cc_start: 0.6442 (t-100) cc_final: 0.5514 (m-10) REVERT: A 123 ASN cc_start: 0.7666 (OUTLIER) cc_final: 0.7427 (m-40) REVERT: A 132 GLU cc_start: 0.7603 (tp30) cc_final: 0.7066 (tt0) REVERT: A 248 GLU cc_start: 0.7324 (mp0) cc_final: 0.7067 (mp0) REVERT: A 344 LYS cc_start: 0.9073 (ttpp) cc_final: 0.8757 (ttpt) REVERT: A 418 ASP cc_start: 0.8333 (m-30) cc_final: 0.8049 (m-30) REVERT: A 465 LYS cc_start: 0.7141 (mptt) cc_final: 0.6698 (tptt) REVERT: A 656 ASP cc_start: 0.7469 (m-30) cc_final: 0.7192 (m-30) outliers start: 26 outliers final: 18 residues processed: 181 average time/residue: 0.1736 time to fit residues: 42.9731 Evaluate side-chains 179 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 461 PHE Chi-restraints excluded: chain A residue 633 ASN Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 682 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.0770 chunk 69 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.157628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.125553 restraints weight = 12541.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.125246 restraints weight = 9515.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.126533 restraints weight = 9117.366| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7437 Z= 0.178 Angle : 0.677 11.687 10065 Z= 0.340 Chirality : 0.041 0.317 1106 Planarity : 0.004 0.050 1257 Dihedral : 4.049 28.510 973 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.05 % Allowed : 22.46 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.29), residues: 866 helix: 2.23 (0.20), residues: 657 sheet: None (None), residues: 0 loop : -2.34 (0.40), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 632 HIS 0.006 0.001 HIS A 122 PHE 0.033 0.001 PHE B 277 TYR 0.014 0.001 TYR A 436 ARG 0.002 0.000 ARG A 589 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3186 (pmm) cc_final: 0.2691 (ptt) REVERT: B 9 GLN cc_start: 0.8425 (mt0) cc_final: 0.8020 (tm-30) REVERT: B 78 GLU cc_start: 0.8398 (pt0) cc_final: 0.8146 (pt0) REVERT: B 83 PHE cc_start: 0.6822 (t80) cc_final: 0.6501 (t80) REVERT: B 85 ARG cc_start: 0.8613 (mmt180) cc_final: 0.7671 (mmm160) REVERT: B 92 ASN cc_start: 0.8645 (t0) cc_final: 0.8420 (t0) REVERT: B 161 ASP cc_start: 0.7266 (OUTLIER) cc_final: 0.6998 (p0) REVERT: B 188 ILE cc_start: 0.8830 (mt) cc_final: 0.8472 (pt) REVERT: B 195 MET cc_start: 0.7586 (mtp) cc_final: 0.7256 (mtt) REVERT: B 197 LEU cc_start: 0.9293 (tp) cc_final: 0.8911 (tp) REVERT: B 271 GLU cc_start: 0.7600 (pt0) cc_final: 0.7301 (pt0) REVERT: B 272 LYS cc_start: 0.8290 (mptt) cc_final: 0.7956 (mmtm) REVERT: B 318 TRP cc_start: 0.6459 (t-100) cc_final: 0.5652 (t-100) REVERT: A 132 GLU cc_start: 0.7646 (tp30) cc_final: 0.7095 (tt0) REVERT: A 152 MET cc_start: 0.8915 (tpp) cc_final: 0.8286 (tpp) REVERT: A 344 LYS cc_start: 0.9084 (ttpp) cc_final: 0.8755 (ttpt) REVERT: A 418 ASP cc_start: 0.8212 (m-30) cc_final: 0.7966 (m-30) REVERT: A 423 ASN cc_start: 0.8459 (p0) cc_final: 0.8152 (p0) REVERT: A 465 LYS cc_start: 0.7052 (mptt) cc_final: 0.6607 (tptt) REVERT: A 656 ASP cc_start: 0.7478 (m-30) cc_final: 0.7206 (m-30) outliers start: 24 outliers final: 21 residues processed: 178 average time/residue: 0.1722 time to fit residues: 42.3830 Evaluate side-chains 179 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 461 PHE Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 633 ASN Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 682 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 29 optimal weight: 0.3980 chunk 46 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 44 optimal weight: 0.0980 chunk 65 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.156799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.125747 restraints weight = 12698.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.124314 restraints weight = 10323.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.125482 restraints weight = 10884.453| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7437 Z= 0.201 Angle : 0.711 10.928 10065 Z= 0.360 Chirality : 0.042 0.308 1106 Planarity : 0.004 0.049 1257 Dihedral : 4.114 28.434 973 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.17 % Allowed : 23.48 % Favored : 73.35 % 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: 1.77 (0.29), residues: 866 helix: 2.20 (0.20), residues: 657 sheet: None (None), residues: 0 loop : -2.37 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 305 HIS 0.005 0.001 HIS B 122 PHE 0.047 0.002 PHE B 147 TYR 0.015 0.001 TYR A 436 ARG 0.002 0.000 ARG A 589 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3114 (pmm) cc_final: 0.2666 (ptt) REVERT: B 9 GLN cc_start: 0.8476 (mt0) cc_final: 0.8068 (tm-30) REVERT: B 78 GLU cc_start: 0.8383 (pt0) cc_final: 0.8124 (pt0) REVERT: B 83 PHE cc_start: 0.6804 (t80) cc_final: 0.6471 (t80) REVERT: B 85 ARG cc_start: 0.8558 (mmt180) cc_final: 0.7696 (mmm160) REVERT: B 92 ASN cc_start: 0.8603 (t0) cc_final: 0.8264 (t0) REVERT: B 161 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6955 (p0) REVERT: B 197 LEU cc_start: 0.9284 (tp) cc_final: 0.8896 (tp) REVERT: B 272 LYS cc_start: 0.8311 (mptt) cc_final: 0.7984 (mmtm) REVERT: B 297 MET cc_start: 0.6101 (OUTLIER) cc_final: 0.5877 (ptm) REVERT: B 318 TRP cc_start: 0.6381 (t-100) cc_final: 0.5571 (t-100) REVERT: A 341 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7174 (mm-30) REVERT: A 344 LYS cc_start: 0.9076 (ttpp) cc_final: 0.8676 (ttpt) REVERT: A 423 ASN cc_start: 0.8431 (p0) cc_final: 0.8119 (p0) REVERT: A 465 LYS cc_start: 0.7005 (mptt) cc_final: 0.6600 (tptt) REVERT: A 656 ASP cc_start: 0.7667 (m-30) cc_final: 0.7410 (m-30) outliers start: 25 outliers final: 18 residues processed: 177 average time/residue: 0.1670 time to fit residues: 41.1215 Evaluate side-chains 178 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 461 PHE Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 633 ASN Chi-restraints excluded: chain A residue 671 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.0870 chunk 0 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.157020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.125834 restraints weight = 12757.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.124268 restraints weight = 11070.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.125838 restraints weight = 11212.324| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7437 Z= 0.200 Angle : 0.721 11.886 10065 Z= 0.361 Chirality : 0.042 0.325 1106 Planarity : 0.004 0.048 1257 Dihedral : 4.091 28.207 973 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.54 % Allowed : 24.24 % Favored : 73.22 % 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: 1.74 (0.29), residues: 866 helix: 2.17 (0.20), residues: 657 sheet: None (None), residues: 0 loop : -2.37 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 305 HIS 0.005 0.001 HIS B 122 PHE 0.037 0.002 PHE B 277 TYR 0.015 0.001 TYR A 436 ARG 0.002 0.000 ARG A 589 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.2936 (pmm) cc_final: 0.2614 (ptt) REVERT: B 9 GLN cc_start: 0.8446 (mt0) cc_final: 0.7997 (tm-30) REVERT: B 78 GLU cc_start: 0.8419 (pt0) cc_final: 0.8160 (pt0) REVERT: B 83 PHE cc_start: 0.6841 (t80) cc_final: 0.6486 (t80) REVERT: B 85 ARG cc_start: 0.8601 (mmt180) cc_final: 0.7775 (mmm160) REVERT: B 92 ASN cc_start: 0.8655 (t0) cc_final: 0.8398 (t0) REVERT: B 161 ASP cc_start: 0.7209 (OUTLIER) cc_final: 0.6938 (p0) REVERT: B 197 LEU cc_start: 0.9335 (tp) cc_final: 0.9044 (tp) REVERT: B 218 GLN cc_start: 0.5837 (mm-40) cc_final: 0.5543 (mm-40) REVERT: B 271 GLU cc_start: 0.7453 (pt0) cc_final: 0.7199 (pt0) REVERT: B 272 LYS cc_start: 0.8294 (mptt) cc_final: 0.7884 (mmtm) REVERT: B 318 TRP cc_start: 0.6405 (t-100) cc_final: 0.5577 (t-100) REVERT: A 132 GLU cc_start: 0.7611 (tp30) cc_final: 0.7051 (tt0) REVERT: A 248 GLU cc_start: 0.7612 (mp0) cc_final: 0.7219 (mp0) REVERT: A 341 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7205 (mm-30) REVERT: A 344 LYS cc_start: 0.9084 (ttpp) cc_final: 0.8684 (ttpt) REVERT: A 423 ASN cc_start: 0.8391 (p0) cc_final: 0.8084 (p0) REVERT: A 465 LYS cc_start: 0.6999 (mptt) cc_final: 0.6591 (tptt) REVERT: A 534 ASP cc_start: 0.8056 (t70) cc_final: 0.7755 (t0) REVERT: A 656 ASP cc_start: 0.7624 (m-30) cc_final: 0.7367 (m-30) outliers start: 20 outliers final: 17 residues processed: 169 average time/residue: 0.1721 time to fit residues: 40.4755 Evaluate side-chains 172 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 461 PHE Chi-restraints excluded: chain A residue 633 ASN Chi-restraints excluded: chain A residue 671 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 66 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 50 optimal weight: 0.0070 chunk 0 optimal weight: 20.0000 chunk 83 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 overall best weight: 0.9204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 GLN A 633 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.156987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.125121 restraints weight = 12478.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.124735 restraints weight = 9141.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.126068 restraints weight = 8840.809| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7437 Z= 0.192 Angle : 0.727 11.802 10065 Z= 0.361 Chirality : 0.042 0.324 1106 Planarity : 0.004 0.047 1257 Dihedral : 4.053 27.485 973 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.54 % Allowed : 25.00 % Favored : 72.46 % 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: 1.78 (0.29), residues: 866 helix: 2.20 (0.20), residues: 657 sheet: None (None), residues: 0 loop : -2.35 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 305 HIS 0.005 0.001 HIS B 122 PHE 0.031 0.001 PHE B 147 TYR 0.014 0.001 TYR A 436 ARG 0.002 0.000 ARG A 589 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2158.29 seconds wall clock time: 39 minutes 27.43 seconds (2367.43 seconds total)