Starting phenix.real_space_refine on Thu Jun 5 01:36:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j3j_61117/06_2025/9j3j_61117.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j3j_61117/06_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_61117/06_2025/9j3j_61117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j3j_61117/06_2025/9j3j_61117.map" model { file = "/net/cci-nas-00/data/ceres_data/9j3j_61117/06_2025/9j3j_61117.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j3j_61117/06_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-5710/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: 3.29, per 1000 atoms: 0.69 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: 1.08 Conformation dependent library (CDL) restraints added in 536.5 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: 0.47 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: 1.39 Time building geometry restraints manager: 1.30 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.940 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:13.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.020 ------------------------------------------------------------------------------- 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 : 0.554 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: 0.9423 time to fit residues: 115.5336 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 : 0.464 ------------------------------------------------------------------------------- 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 = 0.147147 restraints weight = 5679.441| |-----------------------------------------------------------------------------| 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: 0.3450 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- 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 4.94605 ( 1047) SS BOND : bond 0.00199 ( 1) SS BOND : angle 0.76377 ( 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 : 0.497 Fit side-chains REVERT: A 140 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8681 (tt) REVERT: A 290 ARG cc_start: 0.8871 (mmm160) cc_final: 0.8484 (mmm160) REVERT: A 298 LEU cc_start: 0.8704 (tp) cc_final: 0.8425 (tt) REVERT: A 314 LYS cc_start: 0.8454 (mttt) cc_final: 0.8052 (ttmm) REVERT: A 361 PHE cc_start: 0.7570 (t80) cc_final: 0.7335 (t80) REVERT: A 501 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8267 (mm-30) REVERT: B 46 GLU cc_start: 0.8582 (pt0) cc_final: 0.8314 (pt0) outliers start: 9 outliers final: 4 residues processed: 127 average time/residue: 0.9559 time to fit residues: 127.1027 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 : 0.457 ------------------------------------------------------------------------------- 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: 0.0570 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 chunk 44 optimal weight: 0.0040 chunk 26 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.0970 overall best weight: 0.1508 ------------------------------------------------------------------------------- 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 = 0.4129 r_free = 0.4129 target = 0.179506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.154225 restraints weight = 5772.270| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 1.87 r_work: 0.3680 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3556 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4904 Z= 0.118 Angle : 0.526 5.894 6660 Z= 0.270 Chirality : 0.039 0.115 755 Planarity : 0.004 0.039 817 Dihedral : 4.486 20.351 656 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.14 % Allowed : 13.26 % Favored : 84.60 % 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: 1.43 (0.35), residues: 608 helix: 1.76 (0.26), residues: 412 sheet: -0.70 (0.66), residues: 46 loop : -0.72 (0.53), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 258 HIS 0.001 0.000 HIS B 32 PHE 0.018 0.001 PHE A 452 TYR 0.011 0.001 TYR B 54 ARG 0.001 0.000 ARG A 343 Details of bonding type rmsd hydrogen bonds : bond 0.04357 ( 355) hydrogen bonds : angle 4.63497 ( 1047) SS BOND : bond 0.00049 ( 1) SS BOND : angle 0.69984 ( 2) covalent geometry : bond 0.00243 ( 4903) covalent geometry : angle 0.52549 ( 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 123 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.450 Fit side-chains REVERT: A 104 LYS cc_start: 0.8135 (mtpt) cc_final: 0.7862 (mtpm) REVERT: A 140 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8425 (tt) REVERT: A 207 ASN cc_start: 0.8106 (m-40) cc_final: 0.7654 (p0) REVERT: A 290 ARG cc_start: 0.8839 (mmm160) cc_final: 0.8412 (mmm160) REVERT: A 298 LEU cc_start: 0.8499 (tp) cc_final: 0.8236 (tt) REVERT: A 309 TRP cc_start: 0.8385 (t-100) cc_final: 0.8095 (t-100) REVERT: A 361 PHE cc_start: 0.7608 (t80) cc_final: 0.7227 (t80) REVERT: B 46 GLU cc_start: 0.8570 (pt0) cc_final: 0.8351 (pt0) outliers start: 11 outliers final: 4 residues processed: 115 average time/residue: 0.7774 time to fit residues: 94.6368 Evaluate side-chains 104 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 58 optimal weight: 3.9990 chunk 57 optimal weight: 0.0570 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 42 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 B 115 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.173791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.147381 restraints weight = 5797.757| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.94 r_work: 0.3610 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4904 Z= 0.150 Angle : 0.545 5.819 6660 Z= 0.279 Chirality : 0.040 0.123 755 Planarity : 0.004 0.038 817 Dihedral : 4.438 19.625 656 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.12 % Allowed : 15.40 % 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: 1.50 (0.35), residues: 608 helix: 1.75 (0.26), residues: 413 sheet: -0.41 (0.68), residues: 46 loop : -0.60 (0.53), residues: 149 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 0.016 0.002 PHE A 542 TYR 0.011 0.001 TYR B 107 ARG 0.004 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04616 ( 355) hydrogen bonds : angle 4.62016 ( 1047) SS BOND : bond 0.00201 ( 1) SS BOND : angle 0.59929 ( 2) covalent geometry : bond 0.00343 ( 4903) covalent geometry : angle 0.54475 ( 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 133 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.515 Fit side-chains REVERT: A 104 LYS cc_start: 0.8249 (mtpt) cc_final: 0.7920 (mtpm) REVERT: A 140 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8652 (tt) REVERT: A 207 ASN cc_start: 0.8100 (m-40) cc_final: 0.7699 (p0) REVERT: A 239 CYS cc_start: 0.8625 (m) cc_final: 0.8419 (m) REVERT: A 290 ARG cc_start: 0.8863 (mmm160) cc_final: 0.8515 (mmm160) REVERT: A 298 LEU cc_start: 0.8585 (tp) cc_final: 0.8312 (tt) REVERT: A 361 PHE cc_start: 0.7667 (t80) cc_final: 0.7227 (t80) REVERT: A 386 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7882 (tp30) REVERT: A 544 SER cc_start: 0.8348 (OUTLIER) cc_final: 0.8066 (p) REVERT: B 46 GLU cc_start: 0.8595 (pt0) cc_final: 0.8375 (pt0) outliers start: 16 outliers final: 9 residues processed: 122 average time/residue: 0.8223 time to fit residues: 105.8709 Evaluate side-chains 125 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 483 LEU Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 568 LYS Chi-restraints excluded: chain B residue 62 SER 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: 0.6980 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 23 optimal weight: 0.0570 chunk 42 optimal weight: 4.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 547 ASN B 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.176061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.149642 restraints weight = 5883.824| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 1.93 r_work: 0.3618 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4904 Z= 0.138 Angle : 0.551 7.442 6660 Z= 0.275 Chirality : 0.040 0.119 755 Planarity : 0.004 0.040 817 Dihedral : 4.398 19.234 656 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.12 % Allowed : 17.54 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.35), residues: 608 helix: 1.82 (0.26), residues: 413 sheet: -0.23 (0.71), residues: 46 loop : -0.57 (0.52), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 258 HIS 0.000 0.000 HIS A 210 PHE 0.018 0.002 PHE A 542 TYR 0.012 0.001 TYR A 427 ARG 0.005 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04484 ( 355) hydrogen bonds : angle 4.58068 ( 1047) SS BOND : bond 0.00158 ( 1) SS BOND : angle 0.62663 ( 2) covalent geometry : bond 0.00310 ( 4903) covalent geometry : angle 0.55070 ( 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 134 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.586 Fit side-chains REVERT: A 104 LYS cc_start: 0.8247 (mtpt) cc_final: 0.7994 (mtpm) REVERT: A 140 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8618 (tt) REVERT: A 207 ASN cc_start: 0.8002 (m-40) cc_final: 0.7724 (p0) REVERT: A 239 CYS cc_start: 0.8657 (m) cc_final: 0.8413 (m) REVERT: A 290 ARG cc_start: 0.8822 (mmm160) cc_final: 0.8457 (mmm160) REVERT: A 298 LEU cc_start: 0.8582 (tp) cc_final: 0.8320 (tt) REVERT: A 361 PHE cc_start: 0.7631 (t80) cc_final: 0.7174 (t80) REVERT: A 386 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7834 (tp30) REVERT: A 407 MET cc_start: 0.8983 (mmp) cc_final: 0.8497 (mmt) REVERT: A 423 LEU cc_start: 0.8637 (mm) cc_final: 0.8324 (mt) REVERT: B 43 LYS cc_start: 0.8397 (mtpt) cc_final: 0.8128 (mtpp) REVERT: B 46 GLU cc_start: 0.8583 (pt0) cc_final: 0.8347 (pt0) outliers start: 16 outliers final: 9 residues processed: 123 average time/residue: 1.0943 time to fit residues: 141.1162 Evaluate side-chains 126 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 233 LEU 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 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: 2.9990 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 49 optimal weight: 0.1980 chunk 22 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 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 B 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.161060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.134222 restraints weight = 5794.161| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.97 r_work: 0.3447 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1865 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= 0.147 Angle : 0.555 6.051 6660 Z= 0.279 Chirality : 0.040 0.119 755 Planarity : 0.004 0.040 817 Dihedral : 4.378 18.818 656 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.53 % Allowed : 18.52 % Favored : 78.95 % 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: 1.63 (0.35), residues: 608 helix: 1.81 (0.26), residues: 413 sheet: -0.12 (0.71), residues: 46 loop : -0.51 (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 0.021 0.002 PHE A 542 TYR 0.012 0.001 TYR B 54 ARG 0.003 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04537 ( 355) hydrogen bonds : angle 4.58607 ( 1047) SS BOND : bond 0.00072 ( 1) SS BOND : angle 0.75050 ( 2) covalent geometry : bond 0.00338 ( 4903) covalent geometry : angle 0.55510 ( 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 127 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.538 Fit side-chains REVERT: A 104 LYS cc_start: 0.8232 (mtpt) cc_final: 0.7982 (mtpm) REVERT: A 140 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8634 (tt) REVERT: A 207 ASN cc_start: 0.8027 (m-40) cc_final: 0.7766 (p0) REVERT: A 239 CYS cc_start: 0.8691 (m) cc_final: 0.8412 (m) REVERT: A 290 ARG cc_start: 0.8788 (mmm160) cc_final: 0.8415 (mmm160) REVERT: A 298 LEU cc_start: 0.8462 (tp) cc_final: 0.8212 (tt) REVERT: A 361 PHE cc_start: 0.7605 (t80) cc_final: 0.7314 (t80) REVERT: A 386 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7794 (tp30) REVERT: A 407 MET cc_start: 0.8944 (mmp) cc_final: 0.8592 (mmt) REVERT: A 528 LYS cc_start: 0.8103 (mtpt) cc_final: 0.7168 (mptm) REVERT: B 43 LYS cc_start: 0.8365 (mtpt) cc_final: 0.8083 (mtpp) REVERT: B 46 GLU cc_start: 0.8613 (pt0) cc_final: 0.8367 (pt0) outliers start: 13 outliers final: 8 residues processed: 117 average time/residue: 0.8543 time to fit residues: 105.1994 Evaluate side-chains 119 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 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 A residue 577 LEU 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: 0.4980 chunk 49 optimal weight: 0.0070 chunk 8 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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 = 0.3914 r_free = 0.3914 target = 0.162252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.135491 restraints weight = 5762.107| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.96 r_work: 0.3464 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4904 Z= 0.133 Angle : 0.547 7.116 6660 Z= 0.274 Chirality : 0.039 0.125 755 Planarity : 0.004 0.042 817 Dihedral : 4.330 18.643 656 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.92 % Allowed : 18.32 % Favored : 78.75 % 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 (0.35), residues: 608 helix: 1.91 (0.26), residues: 414 sheet: 0.02 (0.72), residues: 46 loop : -0.51 (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 B 32 PHE 0.023 0.001 PHE A 542 TYR 0.013 0.001 TYR B 54 ARG 0.005 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04404 ( 355) hydrogen bonds : angle 4.55167 ( 1047) SS BOND : bond 0.00208 ( 1) SS BOND : angle 0.75278 ( 2) covalent geometry : bond 0.00296 ( 4903) covalent geometry : angle 0.54701 ( 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 133 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.524 Fit side-chains REVERT: A 104 LYS cc_start: 0.8241 (mtpt) cc_final: 0.8004 (mtpm) REVERT: A 207 ASN cc_start: 0.7967 (m-40) cc_final: 0.7722 (p0) REVERT: A 239 CYS cc_start: 0.8700 (m) cc_final: 0.8481 (m) REVERT: A 290 ARG cc_start: 0.8776 (mmm160) cc_final: 0.8389 (mmm160) REVERT: A 298 LEU cc_start: 0.8440 (tp) cc_final: 0.8193 (tt) REVERT: A 343 ARG cc_start: 0.5808 (OUTLIER) cc_final: 0.4943 (mmm160) REVERT: A 361 PHE cc_start: 0.7591 (t80) cc_final: 0.7322 (t80) REVERT: A 386 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7744 (tp30) REVERT: A 407 MET cc_start: 0.8774 (mmp) cc_final: 0.8538 (mmt) REVERT: A 423 LEU cc_start: 0.8582 (mm) cc_final: 0.8278 (mt) REVERT: A 431 LYS cc_start: 0.8325 (tttt) cc_final: 0.8019 (tttm) REVERT: A 528 LYS cc_start: 0.8104 (mtpt) cc_final: 0.7178 (mptm) REVERT: B 43 LYS cc_start: 0.8364 (mtpt) cc_final: 0.8087 (mtpp) REVERT: B 46 GLU cc_start: 0.8597 (pt0) cc_final: 0.8352 (pt0) outliers start: 15 outliers final: 8 residues processed: 123 average time/residue: 1.0399 time to fit residues: 134.3083 Evaluate side-chains 122 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE 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 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: 2.9990 chunk 38 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 35 optimal weight: 0.0980 chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.161458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.134633 restraints weight = 5779.569| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.96 r_work: 0.3451 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2081 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= 0.140 Angle : 0.563 8.567 6660 Z= 0.279 Chirality : 0.040 0.139 755 Planarity : 0.004 0.043 817 Dihedral : 4.321 18.401 656 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.92 % Allowed : 19.10 % Favored : 77.97 % 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: 1.80 (0.35), residues: 608 helix: 1.91 (0.26), residues: 415 sheet: 0.13 (0.71), residues: 46 loop : -0.47 (0.54), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 389 HIS 0.000 0.000 HIS A 210 PHE 0.013 0.001 PHE A 574 TYR 0.013 0.001 TYR B 54 ARG 0.002 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04431 ( 355) hydrogen bonds : angle 4.56596 ( 1047) SS BOND : bond 0.00255 ( 1) SS BOND : angle 0.71626 ( 2) covalent geometry : bond 0.00318 ( 4903) covalent geometry : angle 0.56327 ( 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 132 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.621 Fit side-chains REVERT: A 104 LYS cc_start: 0.8226 (mtpt) cc_final: 0.7991 (mtpm) REVERT: A 207 ASN cc_start: 0.7956 (m-40) cc_final: 0.7754 (p0) REVERT: A 239 CYS cc_start: 0.8762 (m) cc_final: 0.8553 (m) REVERT: A 290 ARG cc_start: 0.8769 (mmm160) cc_final: 0.8372 (mmm160) REVERT: A 298 LEU cc_start: 0.8447 (tp) cc_final: 0.8213 (tt) REVERT: A 343 ARG cc_start: 0.5741 (OUTLIER) cc_final: 0.4885 (mmm160) REVERT: A 361 PHE cc_start: 0.7586 (t80) cc_final: 0.7305 (t80) REVERT: A 386 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7721 (tp30) REVERT: A 423 LEU cc_start: 0.8542 (mm) cc_final: 0.8212 (mt) REVERT: A 431 LYS cc_start: 0.8337 (tttt) cc_final: 0.8021 (tttm) REVERT: A 528 LYS cc_start: 0.8154 (mtpt) cc_final: 0.7221 (mptm) REVERT: B 46 GLU cc_start: 0.8608 (pt0) cc_final: 0.8354 (pt0) outliers start: 15 outliers final: 11 residues processed: 122 average time/residue: 1.1298 time to fit residues: 146.2337 Evaluate side-chains 126 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 233 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 568 LYS Chi-restraints excluded: chain A residue 577 LEU 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: 0.5980 chunk 44 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 0.1980 chunk 8 optimal weight: 0.5980 chunk 59 optimal weight: 0.2980 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 58 optimal weight: 0.2980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.166109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.139187 restraints weight = 5845.955| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.95 r_work: 0.3474 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4904 Z= 0.124 Angle : 0.564 9.245 6660 Z= 0.274 Chirality : 0.040 0.145 755 Planarity : 0.004 0.044 817 Dihedral : 4.273 18.165 656 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.95 % Allowed : 20.47 % Favored : 77.58 % 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: 1.95 (0.35), residues: 608 helix: 2.02 (0.26), residues: 414 sheet: 0.30 (0.72), residues: 46 loop : -0.40 (0.54), residues: 148 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 0.013 0.001 TYR B 54 ARG 0.001 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04263 ( 355) hydrogen bonds : angle 4.53098 ( 1047) SS BOND : bond 0.00209 ( 1) SS BOND : angle 0.70982 ( 2) covalent geometry : bond 0.00272 ( 4903) covalent geometry : angle 0.56402 ( 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 124 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.652 Fit side-chains REVERT: A 247 LEU cc_start: 0.8478 (mt) cc_final: 0.8272 (mt) REVERT: A 290 ARG cc_start: 0.8782 (mmm160) cc_final: 0.8378 (mmm160) REVERT: A 298 LEU cc_start: 0.8451 (tp) cc_final: 0.8212 (tt) REVERT: A 343 ARG cc_start: 0.5713 (OUTLIER) cc_final: 0.4861 (mmm160) REVERT: A 361 PHE cc_start: 0.7601 (t80) cc_final: 0.7332 (t80) REVERT: A 423 LEU cc_start: 0.8568 (mm) cc_final: 0.8246 (mt) REVERT: A 431 LYS cc_start: 0.8256 (tttt) cc_final: 0.7935 (tttm) REVERT: A 528 LYS cc_start: 0.8164 (mtpt) cc_final: 0.7241 (mptm) REVERT: B 3 GLN cc_start: 0.7719 (tp-100) cc_final: 0.7308 (mt0) REVERT: B 46 GLU cc_start: 0.8582 (pt0) cc_final: 0.8351 (pt0) REVERT: B 81 GLN cc_start: 0.8674 (tp40) cc_final: 0.8336 (tp-100) outliers start: 10 outliers final: 8 residues processed: 118 average time/residue: 0.9389 time to fit residues: 116.4960 Evaluate side-chains 119 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 232 ILE 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 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: 0.0970 chunk 47 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3911 r_free = 0.3911 target = 0.163496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.136364 restraints weight = 5794.157| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.92 r_work: 0.3433 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4904 Z= 0.164 Angle : 0.592 9.880 6660 Z= 0.290 Chirality : 0.041 0.146 755 Planarity : 0.004 0.044 817 Dihedral : 4.345 18.194 656 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.75 % Allowed : 20.66 % Favored : 77.58 % 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: 1.83 (0.35), residues: 608 helix: 1.87 (0.25), residues: 418 sheet: 0.36 (0.72), residues: 46 loop : -0.37 (0.56), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 389 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 0.001 0.000 ARG A 299 Details of bonding type rmsd hydrogen bonds : bond 0.04597 ( 355) hydrogen bonds : angle 4.60803 ( 1047) SS BOND : bond 0.00342 ( 1) SS BOND : angle 0.72911 ( 2) covalent geometry : bond 0.00384 ( 4903) covalent geometry : angle 0.59169 ( 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 119 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.471 Fit side-chains REVERT: A 290 ARG cc_start: 0.8799 (mmm160) cc_final: 0.8396 (mmm160) REVERT: A 298 LEU cc_start: 0.8574 (tp) cc_final: 0.8332 (tt) REVERT: A 343 ARG cc_start: 0.5684 (OUTLIER) cc_final: 0.4872 (mmm160) REVERT: A 361 PHE cc_start: 0.7598 (t80) cc_final: 0.7297 (t80) REVERT: A 423 LEU cc_start: 0.8577 (mm) cc_final: 0.8259 (mt) REVERT: A 431 LYS cc_start: 0.8341 (tttt) cc_final: 0.8030 (tttm) REVERT: A 528 LYS cc_start: 0.8167 (mtpt) cc_final: 0.7241 (mptm) REVERT: B 46 GLU cc_start: 0.8591 (pt0) cc_final: 0.8329 (pt0) REVERT: B 81 GLN cc_start: 0.8714 (tp40) cc_final: 0.8505 (tp-100) outliers start: 9 outliers final: 7 residues processed: 115 average time/residue: 0.9474 time to fit residues: 114.2965 Evaluate side-chains 118 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.9990 chunk 27 optimal weight: 0.8980 chunk 51 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 chunk 29 optimal weight: 0.0470 chunk 46 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3926 r_free = 0.3926 target = 0.165173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.138771 restraints weight = 5866.342| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.91 r_work: 0.3449 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4904 Z= 0.127 Angle : 0.571 9.790 6660 Z= 0.277 Chirality : 0.040 0.146 755 Planarity : 0.004 0.045 817 Dihedral : 4.297 17.934 656 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % 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: 2.00 (0.35), residues: 608 helix: 2.03 (0.25), residues: 414 sheet: 0.49 (0.74), 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 0.024 0.001 PHE A 542 TYR 0.014 0.001 TYR B 54 ARG 0.001 0.000 ARG A 299 Details of bonding type rmsd hydrogen bonds : bond 0.04289 ( 355) hydrogen bonds : angle 4.54353 ( 1047) SS BOND : bond 0.00325 ( 1) SS BOND : angle 0.76651 ( 2) covalent geometry : bond 0.00279 ( 4903) covalent geometry : angle 0.57087 ( 6658) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4494.20 seconds wall clock time: 80 minutes 3.52 seconds (4803.52 seconds total)