Starting phenix.real_space_refine on Sat May 10 03:01:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j3j_61117/05_2025/9j3j_61117.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j3j_61117/05_2025/9j3j_61117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j3j_61117/05_2025/9j3j_61117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j3j_61117/05_2025/9j3j_61117.map" model { file = "/net/cci-nas-00/data/ceres_data/9j3j_61117/05_2025/9j3j_61117.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j3j_61117/05_2025/9j3j_61117.cif" } resolution = 2.83 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= 0.081 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 29 5.16 5 C 3152 2.51 5 N 751 2.21 5 O 847 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4779 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3814 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 25, 'TRANS': 464} Chain: "B" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 965 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Time building chain proxies: 3.54, per 1000 atoms: 0.74 Number of scatterers: 4779 At special positions: 0 Unit cell: (79.05, 82.77, 102.3, 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 29 16.00 O 847 8.00 N 751 7.00 C 3152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " 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: 1.18 Conformation dependent library (CDL) restraints added in 558.7 milliseconds 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1128 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 4 sheets defined 72.2% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 110 through 142 Proline residue: A 118 - end of helix removed outlier: 4.252A pdb=" N ASP A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 158 removed outlier: 3.755A pdb=" N PHE A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 178 removed outlier: 3.528A pdb=" N LYS A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 201 Proline residue: A 190 - end of helix Processing helix chain 'A' and resid 205 through 210 removed outlier: 3.526A pdb=" N ILE A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 222 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 226 through 235 removed outlier: 3.566A pdb=" N ILE A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 252 Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 266 through 274 Processing helix chain 'A' and resid 274 through 302 removed outlier: 4.753A pdb=" N GLY A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS A 300 " --> pdb=" O SER A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 338 Processing helix chain 'A' and resid 344 through 348 removed outlier: 4.115A pdb=" N LYS A 348 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 364 Processing helix chain 'A' and resid 365 through 397 Processing helix chain 'A' and resid 399 through 432 removed outlier: 4.371A pdb=" N SER A 411 " --> pdb=" O MET A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 458 removed outlier: 3.541A pdb=" N ALA A 437 " --> pdb=" O GLY A 433 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) Proline residue: A 442 - end of helix Processing helix chain 'A' and resid 458 through 468 removed outlier: 3.846A pdb=" N PHE A 462 " --> pdb=" O PHE A 458 " (cutoff:3.500A) Proline residue: A 464 - end of helix removed outlier: 3.567A pdb=" N LYS A 468 " --> pdb=" O PRO A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 491 Processing helix chain 'A' and resid 495 through 503 removed outlier: 3.820A pdb=" N CYS A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 522 through 543 Processing helix chain 'A' and resid 548 through 590 Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.700A pdb=" N THR B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.692A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 13 361 hydrogen bonds defined for protein. 1047 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.38 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 738 1.29 - 1.42: 1310 1.42 - 1.55: 2805 1.55 - 1.68: 0 1.68 - 1.81: 50 Bond restraints: 4903 Sorted by residual: bond pdb=" C PHE A 542 " pdb=" O PHE A 542 " ideal model delta sigma weight residual 1.233 1.161 0.072 1.43e-02 4.89e+03 2.52e+01 bond pdb=" N TYR B 54 " pdb=" CA TYR B 54 " ideal model delta sigma weight residual 1.456 1.395 0.060 1.33e-02 5.65e+03 2.06e+01 bond pdb=" C TYR B 54 " pdb=" O TYR B 54 " ideal model delta sigma weight residual 1.236 1.179 0.056 1.32e-02 5.74e+03 1.82e+01 bond pdb=" C PHE A 542 " pdb=" N GLY A 543 " ideal model delta sigma weight residual 1.331 1.273 0.058 1.46e-02 4.69e+03 1.57e+01 bond pdb=" CA PHE A 542 " pdb=" CB PHE A 542 " ideal model delta sigma weight residual 1.528 1.475 0.053 1.34e-02 5.57e+03 1.54e+01 ... (remaining 4898 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 6529 2.32 - 4.65: 101 4.65 - 6.97: 26 6.97 - 9.29: 1 9.29 - 11.62: 1 Bond angle restraints: 6658 Sorted by residual: angle pdb=" N PHE A 542 " pdb=" CA PHE A 542 " pdb=" C PHE A 542 " ideal model delta sigma weight residual 111.87 118.59 -6.72 1.41e+00 5.03e-01 2.27e+01 angle pdb=" C THR A 342 " pdb=" N ARG A 343 " pdb=" CA ARG A 343 " ideal model delta sigma weight residual 121.54 129.39 -7.85 1.91e+00 2.74e-01 1.69e+01 angle pdb=" CB MET A 407 " pdb=" CG MET A 407 " pdb=" SD MET A 407 " ideal model delta sigma weight residual 112.70 101.08 11.62 3.00e+00 1.11e-01 1.50e+01 angle pdb=" N PHE A 542 " pdb=" CA PHE A 542 " pdb=" CB PHE A 542 " ideal model delta sigma weight residual 111.39 105.75 5.64 1.56e+00 4.11e-01 1.31e+01 angle pdb=" N TYR B 54 " pdb=" CA TYR B 54 " pdb=" CB TYR B 54 " ideal model delta sigma weight residual 110.46 104.86 5.60 1.57e+00 4.06e-01 1.27e+01 ... (remaining 6653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 2621 16.59 - 33.18: 204 33.18 - 49.77: 38 49.77 - 66.36: 9 66.36 - 82.95: 2 Dihedral angle restraints: 2874 sinusoidal: 1105 harmonic: 1769 Sorted by residual: dihedral pdb=" CA THR A 342 " pdb=" C THR A 342 " pdb=" N ARG A 343 " pdb=" CA ARG A 343 " ideal model delta harmonic sigma weight residual 180.00 154.69 25.31 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ALA A 215 " pdb=" C ALA A 215 " pdb=" N ASP A 216 " pdb=" CA ASP A 216 " ideal model delta harmonic sigma weight residual 180.00 156.14 23.86 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA MET A 407 " pdb=" C MET A 407 " pdb=" N GLY A 408 " pdb=" CA GLY A 408 " ideal model delta harmonic sigma weight residual 180.00 156.60 23.40 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 2871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 493 0.036 - 0.072: 187 0.072 - 0.109: 59 0.109 - 0.145: 10 0.145 - 0.181: 6 Chirality restraints: 755 Sorted by residual: chirality pdb=" CB ILE A 152 " pdb=" CA ILE A 152 " pdb=" CG1 ILE A 152 " pdb=" CG2 ILE A 152 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.19e-01 chirality pdb=" CG LEU A 340 " pdb=" CB LEU A 340 " pdb=" CD1 LEU A 340 " pdb=" CD2 LEU A 340 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" CB ILE A 534 " pdb=" CA ILE A 534 " pdb=" CG1 ILE A 534 " pdb=" CG2 ILE A 534 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 752 not shown) Planarity restraints: 817 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 551 " 0.015 2.00e-02 2.50e+03 1.80e-02 6.48e+00 pdb=" CG TYR A 551 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 551 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 551 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 551 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 551 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 551 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 551 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 541 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.34e+00 pdb=" C SER A 541 " -0.036 2.00e-02 2.50e+03 pdb=" O SER A 541 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE A 542 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 248 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.59e+00 pdb=" C TRP A 248 " 0.033 2.00e-02 2.50e+03 pdb=" O TRP A 248 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 249 " -0.011 2.00e-02 2.50e+03 ... (remaining 814 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 701 2.76 - 3.29: 4881 3.29 - 3.83: 8409 3.83 - 4.36: 9806 4.36 - 4.90: 17002 Nonbonded interactions: 40799 Sorted by model distance: nonbonded pdb=" OE1 GLU A 501 " pdb=" NZ LYS A 516 " model vdw 2.222 3.120 nonbonded pdb=" OE2 GLU A 571 " pdb=" ND2 ASN A 575 " model vdw 2.368 3.120 nonbonded pdb=" O LYS A 314 " pdb=" OG SER A 318 " model vdw 2.368 3.040 nonbonded pdb=" NZ LYS A 115 " pdb=" O ILE A 264 " model vdw 2.387 3.120 nonbonded pdb=" O THR A 388 " pdb=" OG SER A 391 " model vdw 2.424 3.040 ... (remaining 40794 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 15.430 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 4904 Z= 0.241 Angle : 0.732 11.616 6660 Z= 0.393 Chirality : 0.044 0.181 755 Planarity : 0.005 0.045 817 Dihedral : 12.621 82.947 1743 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.18 % 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: -0.36 (0.33), residues: 608 helix: 0.44 (0.25), residues: 406 sheet: -1.32 (0.66), residues: 46 loop : -1.46 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 110 HIS 0.001 0.001 HIS B 32 PHE 0.030 0.002 PHE A 123 TYR 0.044 0.002 TYR A 551 ARG 0.003 0.000 ARG B 66 Details of bonding type rmsd hydrogen bonds : bond 0.12415 ( 355) hydrogen bonds : angle 6.22350 ( 1047) SS BOND : bond 0.00162 ( 1) SS BOND : angle 0.73250 ( 2) covalent geometry : bond 0.00440 ( 4903) covalent geometry : angle 0.73243 ( 6658) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.579 Fit side-chains REVERT: A 290 ARG cc_start: 0.8819 (mmm160) cc_final: 0.8492 (mmm160) REVERT: A 314 LYS cc_start: 0.8344 (mttt) cc_final: 0.7959 (ttmm) REVERT: A 357 GLU cc_start: 0.7760 (tt0) cc_final: 0.7480 (tt0) REVERT: A 361 PHE cc_start: 0.7408 (t80) cc_final: 0.7060 (t80) REVERT: A 544 SER cc_start: 0.8373 (t) cc_final: 0.8131 (p) REVERT: B 81 GLN cc_start: 0.8571 (tp40) cc_final: 0.8358 (tp-100) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.9334 time to fit residues: 114.4603 Evaluate side-chains 111 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 0.0970 chunk 55 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN B 105 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.173532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.147146 restraints weight = 5679.469| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.87 r_work: 0.3579 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 4904 Z= 0.166 Angle : 0.590 6.474 6660 Z= 0.304 Chirality : 0.041 0.129 755 Planarity : 0.005 0.041 817 Dihedral : 4.796 22.026 656 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.75 % Allowed : 10.14 % Favored : 88.11 % 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: 0.65 (0.34), residues: 608 helix: 1.15 (0.25), residues: 413 sheet: -1.06 (0.66), residues: 46 loop : -0.96 (0.52), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 258 HIS 0.001 0.000 HIS A 210 PHE 0.021 0.002 PHE A 123 TYR 0.010 0.001 TYR A 194 ARG 0.002 0.000 ARG A 343 Details of bonding type rmsd hydrogen bonds : bond 0.05171 ( 355) hydrogen bonds : angle 4.94604 ( 1047) SS BOND : bond 0.00199 ( 1) SS BOND : angle 0.76378 ( 2) covalent geometry : bond 0.00377 ( 4903) covalent geometry : angle 0.58984 ( 6658) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.510 Fit side-chains REVERT: A 140 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8683 (tt) REVERT: A 290 ARG cc_start: 0.8870 (mmm160) cc_final: 0.8484 (mmm160) REVERT: A 298 LEU cc_start: 0.8702 (tp) cc_final: 0.8424 (tt) REVERT: A 314 LYS cc_start: 0.8452 (mttt) cc_final: 0.8050 (ttmm) REVERT: A 361 PHE cc_start: 0.7571 (t80) cc_final: 0.7337 (t80) REVERT: A 501 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8266 (mm-30) REVERT: B 46 GLU cc_start: 0.8585 (pt0) cc_final: 0.8317 (pt0) outliers start: 9 outliers final: 4 residues processed: 127 average time/residue: 0.9030 time to fit residues: 120.1948 Evaluate side-chains 125 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 120 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 568 LYS Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 118 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.0060 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN A 301 ASN A 524 ASN B 81 GLN B 105 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.174344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.148067 restraints weight = 5748.749| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.90 r_work: 0.3597 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4904 Z= 0.150 Angle : 0.555 5.862 6660 Z= 0.286 Chirality : 0.040 0.120 755 Planarity : 0.004 0.040 817 Dihedral : 4.615 20.816 656 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.53 % Allowed : 12.28 % Favored : 85.19 % 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: 1.15 (0.34), residues: 608 helix: 1.55 (0.26), residues: 410 sheet: -0.89 (0.65), residues: 46 loop : -0.77 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 258 HIS 0.001 0.000 HIS B 32 PHE 0.015 0.002 PHE A 452 TYR 0.009 0.001 TYR A 194 ARG 0.001 0.000 ARG A 343 Details of bonding type rmsd hydrogen bonds : bond 0.04840 ( 355) hydrogen bonds : angle 4.78912 ( 1047) SS BOND : bond 0.00162 ( 1) SS BOND : angle 0.70018 ( 2) covalent geometry : bond 0.00340 ( 4903) covalent geometry : angle 0.55527 ( 6658) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.579 Fit side-chains REVERT: A 140 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8671 (tt) REVERT: A 290 ARG cc_start: 0.8855 (mmm160) cc_final: 0.8455 (mmm160) REVERT: A 298 LEU cc_start: 0.8726 (tp) cc_final: 0.8449 (tt) REVERT: A 300 LYS cc_start: 0.8482 (mppt) cc_final: 0.8202 (mppt) REVERT: A 361 PHE cc_start: 0.7654 (t80) cc_final: 0.7423 (t80) REVERT: A 386 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7877 (tp30) REVERT: A 501 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8382 (mm-30) REVERT: B 46 GLU cc_start: 0.8610 (pt0) cc_final: 0.8359 (pt0) outliers start: 13 outliers final: 6 residues processed: 124 average time/residue: 0.8857 time to fit residues: 115.3446 Evaluate side-chains 124 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 568 LYS Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 118 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 0.3980 chunk 49 optimal weight: 0.2980 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 524 ASN B 81 GLN B 115 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.174822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.148453 restraints weight = 5803.983| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.91 r_work: 0.3611 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4904 Z= 0.144 Angle : 0.556 7.150 6660 Z= 0.281 Chirality : 0.040 0.120 755 Planarity : 0.004 0.039 817 Dihedral : 4.521 20.090 656 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.34 % Allowed : 16.18 % Favored : 81.48 % 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: 1.36 (0.34), residues: 608 helix: 1.67 (0.26), residues: 413 sheet: -0.59 (0.67), residues: 46 loop : -0.66 (0.52), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 258 HIS 0.000 0.000 HIS A 210 PHE 0.016 0.002 PHE A 542 TYR 0.011 0.001 TYR A 551 ARG 0.004 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04665 ( 355) hydrogen bonds : angle 4.70139 ( 1047) SS BOND : bond 0.00144 ( 1) SS BOND : angle 0.52018 ( 2) covalent geometry : bond 0.00324 ( 4903) covalent geometry : angle 0.55647 ( 6658) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.499 Fit side-chains REVERT: A 104 LYS cc_start: 0.8300 (mtpt) cc_final: 0.8085 (mtpm) REVERT: A 140 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8672 (tt) REVERT: A 290 ARG cc_start: 0.8886 (mmm160) cc_final: 0.8466 (mmm160) REVERT: A 298 LEU cc_start: 0.8715 (tp) cc_final: 0.8430 (tt) REVERT: A 300 LYS cc_start: 0.8488 (mppt) cc_final: 0.8253 (mppt) REVERT: A 361 PHE cc_start: 0.7704 (t80) cc_final: 0.7426 (t80) REVERT: A 386 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7882 (tp30) REVERT: B 46 GLU cc_start: 0.8573 (pt0) cc_final: 0.8331 (pt0) outliers start: 12 outliers final: 8 residues processed: 121 average time/residue: 0.8338 time to fit residues: 106.1995 Evaluate side-chains 123 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 568 LYS Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 118 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 38 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 48 optimal weight: 8.9990 chunk 23 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN B 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.174387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.147922 restraints weight = 5890.819| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.93 r_work: 0.3590 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4904 Z= 0.151 Angle : 0.558 5.790 6660 Z= 0.282 Chirality : 0.040 0.120 755 Planarity : 0.004 0.039 817 Dihedral : 4.484 19.655 656 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.12 % Allowed : 16.57 % Favored : 80.31 % 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: 1.48 (0.35), residues: 608 helix: 1.73 (0.26), residues: 413 sheet: -0.40 (0.70), residues: 46 loop : -0.59 (0.52), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 258 HIS 0.001 0.000 HIS A 210 PHE 0.013 0.002 PHE A 574 TYR 0.012 0.001 TYR B 54 ARG 0.002 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04666 ( 355) hydrogen bonds : angle 4.65659 ( 1047) SS BOND : bond 0.00204 ( 1) SS BOND : angle 0.56889 ( 2) covalent geometry : bond 0.00346 ( 4903) covalent geometry : angle 0.55832 ( 6658) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.569 Fit side-chains REVERT: A 104 LYS cc_start: 0.8309 (mtpt) cc_final: 0.8069 (mtpm) REVERT: A 140 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8688 (tt) REVERT: A 207 ASN cc_start: 0.8202 (m-40) cc_final: 0.7753 (p0) REVERT: A 290 ARG cc_start: 0.8853 (mmm160) cc_final: 0.8510 (mmm160) REVERT: A 298 LEU cc_start: 0.8694 (tp) cc_final: 0.8421 (tt) REVERT: A 300 LYS cc_start: 0.8470 (mppt) cc_final: 0.8230 (mppt) REVERT: A 361 PHE cc_start: 0.7684 (t80) cc_final: 0.7398 (t80) REVERT: A 386 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7881 (tp30) REVERT: A 423 LEU cc_start: 0.8655 (mm) cc_final: 0.8334 (mt) REVERT: B 46 GLU cc_start: 0.8594 (pt0) cc_final: 0.8342 (pt0) outliers start: 16 outliers final: 9 residues processed: 125 average time/residue: 0.8839 time to fit residues: 116.3243 Evaluate side-chains 123 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 568 LYS Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 118 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 12 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 49 optimal weight: 0.0170 chunk 22 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 56 optimal weight: 0.0970 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN B 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.161063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.134288 restraints weight = 5802.513| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.96 r_work: 0.3452 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4904 Z= 0.137 Angle : 0.555 6.269 6660 Z= 0.278 Chirality : 0.040 0.115 755 Planarity : 0.004 0.041 817 Dihedral : 4.409 19.197 656 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.12 % Allowed : 16.76 % Favored : 80.12 % 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: 1.60 (0.35), residues: 608 helix: 1.78 (0.26), residues: 414 sheet: -0.15 (0.72), residues: 46 loop : -0.54 (0.53), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 258 HIS 0.000 0.000 HIS A 210 PHE 0.021 0.002 PHE A 542 TYR 0.013 0.001 TYR B 54 ARG 0.002 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04524 ( 355) hydrogen bonds : angle 4.60745 ( 1047) SS BOND : bond 0.00143 ( 1) SS BOND : angle 0.54118 ( 2) covalent geometry : bond 0.00306 ( 4903) covalent geometry : angle 0.55485 ( 6658) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.552 Fit side-chains REVERT: A 104 LYS cc_start: 0.8242 (mtpt) cc_final: 0.7999 (mtpm) REVERT: A 140 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8622 (tt) REVERT: A 207 ASN cc_start: 0.8173 (m-40) cc_final: 0.7779 (p0) REVERT: A 263 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8672 (pt0) REVERT: A 290 ARG cc_start: 0.8788 (mmm160) cc_final: 0.8427 (mmm160) REVERT: A 298 LEU cc_start: 0.8533 (tp) cc_final: 0.8275 (tt) REVERT: A 300 LYS cc_start: 0.8403 (mppt) cc_final: 0.8172 (mppt) REVERT: A 361 PHE cc_start: 0.7597 (t80) cc_final: 0.7096 (t80) REVERT: A 386 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7783 (tp30) REVERT: B 43 LYS cc_start: 0.8405 (mtpt) cc_final: 0.8123 (mtpp) REVERT: B 46 GLU cc_start: 0.8600 (pt0) cc_final: 0.8345 (pt0) outliers start: 16 outliers final: 9 residues processed: 126 average time/residue: 0.8545 time to fit residues: 113.2788 Evaluate side-chains 124 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 118 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 0.9990 chunk 49 optimal weight: 0.0070 chunk 8 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.161202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.134903 restraints weight = 5717.580| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.90 r_work: 0.3373 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4904 Z= 0.146 Angle : 0.564 7.156 6660 Z= 0.282 Chirality : 0.040 0.117 755 Planarity : 0.004 0.042 817 Dihedral : 4.388 18.875 656 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.12 % Allowed : 18.52 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.35), residues: 608 helix: 1.80 (0.26), residues: 414 sheet: -0.09 (0.72), residues: 46 loop : -0.55 (0.53), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 258 HIS 0.001 0.000 HIS A 210 PHE 0.023 0.002 PHE A 542 TYR 0.014 0.001 TYR B 54 ARG 0.002 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04598 ( 355) hydrogen bonds : angle 4.60862 ( 1047) SS BOND : bond 0.00184 ( 1) SS BOND : angle 0.54751 ( 2) covalent geometry : bond 0.00334 ( 4903) covalent geometry : angle 0.56427 ( 6658) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.558 Fit side-chains REVERT: A 104 LYS cc_start: 0.8236 (mtpt) cc_final: 0.8000 (mtpm) REVERT: A 207 ASN cc_start: 0.8051 (m-40) cc_final: 0.7752 (p0) REVERT: A 290 ARG cc_start: 0.8815 (mmm160) cc_final: 0.8455 (mmm160) REVERT: A 298 LEU cc_start: 0.8555 (tp) cc_final: 0.8304 (tt) REVERT: A 300 LYS cc_start: 0.8407 (mppt) cc_final: 0.8181 (mppt) REVERT: A 343 ARG cc_start: 0.5925 (OUTLIER) cc_final: 0.4987 (mmm160) REVERT: A 361 PHE cc_start: 0.7587 (t80) cc_final: 0.7316 (t80) REVERT: A 386 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7805 (tp30) REVERT: A 407 MET cc_start: 0.8944 (mmp) cc_final: 0.8532 (mmt) REVERT: A 423 LEU cc_start: 0.8605 (mm) cc_final: 0.8310 (mt) REVERT: A 528 LYS cc_start: 0.8135 (mtpt) cc_final: 0.7208 (mptm) REVERT: B 43 LYS cc_start: 0.8417 (mtpt) cc_final: 0.8141 (mtpp) REVERT: B 46 GLU cc_start: 0.8603 (pt0) cc_final: 0.8336 (pt0) outliers start: 16 outliers final: 11 residues processed: 118 average time/residue: 0.9285 time to fit residues: 114.9945 Evaluate side-chains 122 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 568 LYS Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 118 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 50 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 0.1980 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 301 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.163544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.136424 restraints weight = 5797.911| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.95 r_work: 0.3416 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4904 Z= 0.148 Angle : 0.568 8.092 6660 Z= 0.283 Chirality : 0.040 0.135 755 Planarity : 0.004 0.043 817 Dihedral : 4.379 18.642 656 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.92 % Allowed : 18.71 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.34), residues: 608 helix: 1.83 (0.25), residues: 414 sheet: -0.09 (0.70), residues: 46 loop : -0.53 (0.53), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 258 HIS 0.001 0.001 HIS B 32 PHE 0.024 0.002 PHE A 542 TYR 0.013 0.001 TYR B 54 ARG 0.004 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04586 ( 355) hydrogen bonds : angle 4.60869 ( 1047) SS BOND : bond 0.00227 ( 1) SS BOND : angle 0.62857 ( 2) covalent geometry : bond 0.00338 ( 4903) covalent geometry : angle 0.56844 ( 6658) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.595 Fit side-chains REVERT: A 104 LYS cc_start: 0.8226 (mtpt) cc_final: 0.7995 (mtpm) REVERT: A 114 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8264 (ptmt) REVERT: A 207 ASN cc_start: 0.8003 (m-40) cc_final: 0.7782 (p0) REVERT: A 290 ARG cc_start: 0.8793 (mmm160) cc_final: 0.8427 (mmm160) REVERT: A 298 LEU cc_start: 0.8548 (tp) cc_final: 0.8298 (tt) REVERT: A 300 LYS cc_start: 0.8394 (mppt) cc_final: 0.8167 (mppt) REVERT: A 343 ARG cc_start: 0.5808 (OUTLIER) cc_final: 0.4910 (mmm160) REVERT: A 361 PHE cc_start: 0.7567 (t80) cc_final: 0.7283 (t80) REVERT: A 386 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7781 (tp30) REVERT: A 423 LEU cc_start: 0.8567 (mm) cc_final: 0.8243 (mt) REVERT: A 431 LYS cc_start: 0.8354 (tttt) cc_final: 0.8045 (tttm) REVERT: A 528 LYS cc_start: 0.8139 (mtpt) cc_final: 0.7213 (mptm) REVERT: B 43 LYS cc_start: 0.8393 (mtpt) cc_final: 0.8126 (mtpp) REVERT: B 46 GLU cc_start: 0.8588 (pt0) cc_final: 0.8315 (pt0) outliers start: 15 outliers final: 11 residues processed: 120 average time/residue: 1.0010 time to fit residues: 126.4863 Evaluate side-chains 125 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 568 LYS Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 118 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 35 optimal weight: 0.0770 chunk 44 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 57 optimal weight: 0.2980 chunk 8 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 535 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.162089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.135333 restraints weight = 5797.795| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.97 r_work: 0.3387 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4904 Z= 0.130 Angle : 0.559 9.273 6660 Z= 0.276 Chirality : 0.040 0.151 755 Planarity : 0.004 0.045 817 Dihedral : 4.326 18.394 656 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.34 % Allowed : 20.27 % Favored : 77.39 % 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: 1.93 (0.35), residues: 608 helix: 2.03 (0.26), residues: 409 sheet: 0.14 (0.72), residues: 46 loop : -0.38 (0.53), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 258 HIS 0.001 0.000 HIS B 32 PHE 0.025 0.001 PHE A 542 TYR 0.014 0.001 TYR B 54 ARG 0.001 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04380 ( 355) hydrogen bonds : angle 4.55760 ( 1047) SS BOND : bond 0.00106 ( 1) SS BOND : angle 0.51612 ( 2) covalent geometry : bond 0.00290 ( 4903) covalent geometry : angle 0.55888 ( 6658) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.533 Fit side-chains REVERT: A 104 LYS cc_start: 0.8199 (mtpt) cc_final: 0.7966 (mtpm) REVERT: A 290 ARG cc_start: 0.8776 (mmm160) cc_final: 0.8401 (mmm160) REVERT: A 298 LEU cc_start: 0.8399 (tp) cc_final: 0.8178 (tt) REVERT: A 300 LYS cc_start: 0.8409 (mppt) cc_final: 0.8177 (mppt) REVERT: A 343 ARG cc_start: 0.5804 (OUTLIER) cc_final: 0.4895 (mmm160) REVERT: A 361 PHE cc_start: 0.7574 (t80) cc_final: 0.7272 (t80) REVERT: A 386 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7712 (tp30) REVERT: A 423 LEU cc_start: 0.8563 (mm) cc_final: 0.8247 (mt) REVERT: A 431 LYS cc_start: 0.8311 (tttt) cc_final: 0.8008 (tttm) REVERT: A 528 LYS cc_start: 0.8106 (mtpt) cc_final: 0.7176 (mptm) REVERT: B 46 GLU cc_start: 0.8602 (pt0) cc_final: 0.8338 (pt0) outliers start: 12 outliers final: 7 residues processed: 125 average time/residue: 0.8892 time to fit residues: 117.0291 Evaluate side-chains 121 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain B residue 118 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 40 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 39 optimal weight: 0.0870 chunk 48 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.163552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.136360 restraints weight = 5786.450| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.93 r_work: 0.3418 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4904 Z= 0.155 Angle : 0.579 9.618 6660 Z= 0.286 Chirality : 0.041 0.145 755 Planarity : 0.005 0.045 817 Dihedral : 4.357 18.359 656 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.95 % Allowed : 21.25 % Favored : 76.80 % 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: 1.79 (0.35), residues: 608 helix: 1.90 (0.25), residues: 414 sheet: 0.04 (0.70), residues: 46 loop : -0.41 (0.53), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 389 HIS 0.001 0.000 HIS B 32 PHE 0.025 0.002 PHE A 542 TYR 0.014 0.001 TYR B 107 ARG 0.001 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04557 ( 355) hydrogen bonds : angle 4.60894 ( 1047) SS BOND : bond 0.00251 ( 1) SS BOND : angle 0.73912 ( 2) covalent geometry : bond 0.00360 ( 4903) covalent geometry : angle 0.57939 ( 6658) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.488 Fit side-chains REVERT: A 104 LYS cc_start: 0.8221 (mtpt) cc_final: 0.7997 (mtpm) REVERT: A 290 ARG cc_start: 0.8803 (mmm160) cc_final: 0.8426 (mmm160) REVERT: A 298 LEU cc_start: 0.8550 (tp) cc_final: 0.8313 (tt) REVERT: A 300 LYS cc_start: 0.8443 (mppt) cc_final: 0.8224 (mppt) REVERT: A 343 ARG cc_start: 0.5814 (OUTLIER) cc_final: 0.4941 (mmm160) REVERT: A 361 PHE cc_start: 0.7588 (t80) cc_final: 0.7323 (t80) REVERT: A 386 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7767 (tp30) REVERT: A 423 LEU cc_start: 0.8594 (mm) cc_final: 0.8287 (mt) REVERT: A 431 LYS cc_start: 0.8332 (tttt) cc_final: 0.8026 (tttm) REVERT: A 528 LYS cc_start: 0.8144 (mtpt) cc_final: 0.7225 (mptm) REVERT: B 46 GLU cc_start: 0.8587 (pt0) cc_final: 0.8318 (pt0) REVERT: B 81 GLN cc_start: 0.8649 (tp40) cc_final: 0.8431 (tp-100) outliers start: 10 outliers final: 7 residues processed: 115 average time/residue: 0.9016 time to fit residues: 108.8514 Evaluate side-chains 119 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain B residue 118 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 57 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.0050 chunk 46 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.164017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.136933 restraints weight = 5886.754| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.95 r_work: 0.3449 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4904 Z= 0.135 Angle : 0.575 9.441 6660 Z= 0.280 Chirality : 0.040 0.146 755 Planarity : 0.004 0.045 817 Dihedral : 4.339 18.392 656 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.75 % Allowed : 21.64 % Favored : 76.61 % 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: 1.88 (0.35), residues: 608 helix: 1.94 (0.25), residues: 414 sheet: 0.35 (0.72), residues: 46 loop : -0.37 (0.54), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 389 HIS 0.000 0.000 HIS A 210 PHE 0.025 0.001 PHE A 542 TYR 0.014 0.001 TYR B 54 ARG 0.001 0.000 ARG A 578 Details of bonding type rmsd hydrogen bonds : bond 0.04394 ( 355) hydrogen bonds : angle 4.56577 ( 1047) SS BOND : bond 0.00369 ( 1) SS BOND : angle 0.73442 ( 2) covalent geometry : bond 0.00305 ( 4903) covalent geometry : angle 0.57487 ( 6658) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3885.17 seconds wall clock time: 67 minutes 45.25 seconds (4065.25 seconds total)