Starting phenix.real_space_refine on Thu Mar 13 06:20:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pla_13486/03_2025/7pla_13486_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pla_13486/03_2025/7pla_13486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pla_13486/03_2025/7pla_13486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pla_13486/03_2025/7pla_13486.map" model { file = "/net/cci-nas-00/data/ceres_data/7pla_13486/03_2025/7pla_13486_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pla_13486/03_2025/7pla_13486_neut.cif" } resolution = 3.04 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= 0.005 sd= 0.013 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: 5 Type Number sf(0) Gaussians P 243 5.49 5 S 11 5.16 5 C 4560 2.51 5 N 1555 2.21 5 O 2332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8701 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3533 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 420} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 4619 Classifications: {'RNA': 217} Modifications used: {'rna2p_pur': 18, 'rna2p_pyr': 18, 'rna3p_pur': 92, 'rna3p_pyr': 89} Link IDs: {'rna2p': 36, 'rna3p': 180} Chain breaks: 3 Chain: "C" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 339 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "D" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 210 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.78, per 1000 atoms: 0.66 Number of scatterers: 8701 At special positions: 0 Unit cell: (99.84, 92.8, 116.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 P 243 15.00 O 2332 8.00 N 1555 7.00 C 4560 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 487.5 milliseconds 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 826 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 2 sheets defined 56.5% alpha, 15.3% beta 89 base pairs and 155 stacking pairs defined. Time for finding SS restraints: 4.45 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 Proline residue: A 30 - end of helix removed outlier: 3.709A pdb=" N ASN A 33 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLN A 41 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N HIS A 42 " --> pdb=" O GLN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 69 removed outlier: 3.779A pdb=" N GLN A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) Proline residue: A 65 - end of helix removed outlier: 4.414A pdb=" N THR A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASP A 69 " --> pdb=" O PRO A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 92 removed outlier: 3.593A pdb=" N MET A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE A 84 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 339 removed outlier: 4.048A pdb=" N PHE A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 347 removed outlier: 3.604A pdb=" N LEU A 346 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 343 through 347' Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 407 Processing helix chain 'A' and resid 413 through 430 removed outlier: 4.096A pdb=" N ASN A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'A' and resid 485 through 506 removed outlier: 3.591A pdb=" N GLN A 506 " --> pdb=" O ARG A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 538 removed outlier: 3.661A pdb=" N ALA A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 551 Processing helix chain 'A' and resid 552 through 567 Processing helix chain 'A' and resid 570 through 585 Processing helix chain 'A' and resid 591 through 605 Processing helix chain 'A' and resid 618 through 636 removed outlier: 3.830A pdb=" N THR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 283 through 285 removed outlier: 6.708A pdb=" N LEU A 349 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASP A 378 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN A 351 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU A 371 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 10 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LEU A 301 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 471 through 475 removed outlier: 6.835A pdb=" N VAL A 463 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N TYR A 474 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL A 461 " --> pdb=" O TYR A 474 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N SER A 445 " --> pdb=" O ALA A 540 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N SER A 542 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE A 447 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N VAL A 544 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A 449 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N VAL A 451 " --> pdb=" O PRO A 546 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL A 607 " --> pdb=" O GLY A 541 " (cutoff:3.500A) 202 hydrogen bonds defined for protein. 597 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 224 hydrogen bonds 412 hydrogen bond angles 0 basepair planarities 89 basepair parallelities 155 stacking parallelities Total time for adding SS restraints: 4.42 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 958 1.32 - 1.44: 3816 1.44 - 1.56: 4107 1.56 - 1.69: 477 1.69 - 1.81: 16 Bond restraints: 9374 Sorted by residual: bond pdb=" O3' G B 230 " pdb=" P G B 231 " ideal model delta sigma weight residual 1.607 1.557 0.050 1.50e-02 4.44e+03 1.12e+01 bond pdb=" N GLY A 359 " pdb=" CA GLY A 359 " ideal model delta sigma weight residual 1.445 1.477 -0.032 9.90e-03 1.02e+04 1.06e+01 bond pdb=" O3' G B 40 " pdb=" P A B 41 " ideal model delta sigma weight residual 1.607 1.559 0.048 1.50e-02 4.44e+03 1.04e+01 bond pdb=" C PRO A 365 " pdb=" O PRO A 365 " ideal model delta sigma weight residual 1.238 1.195 0.043 1.36e-02 5.41e+03 9.91e+00 bond pdb=" O3' A B 229 " pdb=" P G B 230 " ideal model delta sigma weight residual 1.607 1.560 0.047 1.50e-02 4.44e+03 9.85e+00 ... (remaining 9369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 12548 1.74 - 3.47: 994 3.47 - 5.21: 249 5.21 - 6.94: 30 6.94 - 8.68: 11 Bond angle restraints: 13832 Sorted by residual: angle pdb=" N ASN A 367 " pdb=" CA ASN A 367 " pdb=" C ASN A 367 " ideal model delta sigma weight residual 111.75 103.96 7.79 1.28e+00 6.10e-01 3.71e+01 angle pdb=" O3' A B 130 " pdb=" C3' A B 130 " pdb=" C2' A B 130 " ideal model delta sigma weight residual 109.50 117.81 -8.31 1.50e+00 4.44e-01 3.07e+01 angle pdb=" O3' G B 86 " pdb=" C3' G B 86 " pdb=" C2' G B 86 " ideal model delta sigma weight residual 109.50 101.27 8.23 1.50e+00 4.44e-01 3.01e+01 angle pdb=" O3' U B 98 " pdb=" C3' U B 98 " pdb=" C2' U B 98 " ideal model delta sigma weight residual 109.50 117.71 -8.21 1.50e+00 4.44e-01 3.00e+01 angle pdb=" C4' G B 230 " pdb=" C3' G B 230 " pdb=" O3' G B 230 " ideal model delta sigma weight residual 113.00 104.98 8.02 1.50e+00 4.44e-01 2.86e+01 ... (remaining 13827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 5020 35.80 - 71.59: 744 71.59 - 107.39: 75 107.39 - 143.19: 3 143.19 - 178.99: 9 Dihedral angle restraints: 5851 sinusoidal: 4577 harmonic: 1274 Sorted by residual: dihedral pdb=" O4' U B 84 " pdb=" C1' U B 84 " pdb=" N1 U B 84 " pdb=" C2 U B 84 " ideal model delta sinusoidal sigma weight residual 200.00 25.83 174.17 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" C5' U B 98 " pdb=" C4' U B 98 " pdb=" C3' U B 98 " pdb=" O3' U B 98 " ideal model delta sinusoidal sigma weight residual 147.00 87.55 59.45 1 8.00e+00 1.56e-02 7.37e+01 dihedral pdb=" O4' U B 8 " pdb=" C1' U B 8 " pdb=" N1 U B 8 " pdb=" C2 U B 8 " ideal model delta sinusoidal sigma weight residual -160.00 -34.81 -125.19 1 1.50e+01 4.44e-03 6.73e+01 ... (remaining 5848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 1363 0.116 - 0.232: 343 0.232 - 0.347: 14 0.347 - 0.463: 2 0.463 - 0.579: 2 Chirality restraints: 1724 Sorted by residual: chirality pdb=" P G B 174 " pdb=" OP1 G B 174 " pdb=" OP2 G B 174 " pdb=" O5' G B 174 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.38e+00 chirality pdb=" P G B 221 " pdb=" OP1 G B 221 " pdb=" OP2 G B 221 " pdb=" O5' G B 221 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.47e+00 chirality pdb=" C3' A B 130 " pdb=" C4' A B 130 " pdb=" O3' A B 130 " pdb=" C2' A B 130 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.37 2.00e-01 2.50e+01 3.51e+00 ... (remaining 1721 not shown) Planarity restraints: 870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U B 101 " -0.045 2.00e-02 2.50e+03 2.37e-02 1.26e+01 pdb=" N1 U B 101 " 0.051 2.00e-02 2.50e+03 pdb=" C2 U B 101 " 0.009 2.00e-02 2.50e+03 pdb=" O2 U B 101 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U B 101 " -0.004 2.00e-02 2.50e+03 pdb=" C4 U B 101 " -0.014 2.00e-02 2.50e+03 pdb=" O4 U B 101 " -0.007 2.00e-02 2.50e+03 pdb=" C5 U B 101 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U B 101 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 45 " -0.032 2.00e-02 2.50e+03 1.81e-02 7.38e+00 pdb=" N1 U B 45 " 0.040 2.00e-02 2.50e+03 pdb=" C2 U B 45 " 0.007 2.00e-02 2.50e+03 pdb=" O2 U B 45 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U B 45 " -0.007 2.00e-02 2.50e+03 pdb=" C4 U B 45 " -0.008 2.00e-02 2.50e+03 pdb=" O4 U B 45 " -0.002 2.00e-02 2.50e+03 pdb=" C5 U B 45 " -0.007 2.00e-02 2.50e+03 pdb=" C6 U B 45 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 44 " -0.029 2.00e-02 2.50e+03 1.56e-02 5.50e+00 pdb=" N1 U B 44 " 0.035 2.00e-02 2.50e+03 pdb=" C2 U B 44 " 0.005 2.00e-02 2.50e+03 pdb=" O2 U B 44 " -0.001 2.00e-02 2.50e+03 pdb=" N3 U B 44 " 0.000 2.00e-02 2.50e+03 pdb=" C4 U B 44 " -0.004 2.00e-02 2.50e+03 pdb=" O4 U B 44 " -0.008 2.00e-02 2.50e+03 pdb=" C5 U B 44 " -0.003 2.00e-02 2.50e+03 pdb=" C6 U B 44 " 0.005 2.00e-02 2.50e+03 ... (remaining 867 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1367 2.75 - 3.29: 7522 3.29 - 3.83: 18158 3.83 - 4.36: 22029 4.36 - 4.90: 28991 Nonbonded interactions: 78067 Sorted by model distance: nonbonded pdb=" OG SER A 424 " pdb=" NH1 ARG A 428 " model vdw 2.216 3.120 nonbonded pdb=" OG SER A 77 " pdb=" C5' DG D 16 " model vdw 2.234 3.440 nonbonded pdb=" O GLY A 454 " pdb=" OH TYR A 590 " model vdw 2.257 3.040 nonbonded pdb=" O TRP A 293 " pdb=" NE2 GLN A 332 " model vdw 2.258 3.120 nonbonded pdb=" NZ LYS A 547 " pdb=" OE1 GLU A 610 " model vdw 2.284 3.120 ... (remaining 78062 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: 0.010 Normalize map: mean=0, sd=1: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.820 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5863 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 : 0.008 0.050 9374 Z= 0.448 Angle : 1.084 8.680 13832 Z= 0.712 Chirality : 0.092 0.579 1724 Planarity : 0.005 0.031 870 Dihedral : 26.236 178.987 5025 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.26 % Allowed : 0.52 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.41), residues: 429 helix: 1.11 (0.34), residues: 231 sheet: -1.19 (0.63), residues: 70 loop : -1.32 (0.56), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 94 HIS 0.009 0.001 HIS A 342 PHE 0.017 0.002 PHE A 347 TYR 0.011 0.001 TYR A 474 ARG 0.012 0.001 ARG A 17 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.555 Fit side-chains REVERT: A 81 MET cc_start: 0.8943 (tpt) cc_final: 0.8503 (tpp) REVERT: A 347 PHE cc_start: 0.8227 (m-80) cc_final: 0.7981 (m-80) outliers start: 1 outliers final: 0 residues processed: 13 average time/residue: 0.2844 time to fit residues: 5.5587 Evaluate side-chains 11 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 20 optimal weight: 30.0000 chunk 31 optimal weight: 30.0000 chunk 38 optimal weight: 0.8980 chunk 59 optimal weight: 20.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.064510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.046299 restraints weight = 47330.079| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.25 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9374 Z= 0.286 Angle : 0.688 7.287 13832 Z= 0.355 Chirality : 0.039 0.265 1724 Planarity : 0.005 0.032 870 Dihedral : 26.548 178.721 4135 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.04 % Allowed : 5.44 % Favored : 93.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.41), residues: 429 helix: 1.75 (0.33), residues: 226 sheet: -1.61 (0.55), residues: 79 loop : -1.19 (0.59), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 366 HIS 0.003 0.001 HIS A 522 PHE 0.010 0.002 PHE A 313 TYR 0.010 0.002 TYR A 80 ARG 0.006 0.001 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.550 Fit side-chains REVERT: A 35 LEU cc_start: 0.9374 (mt) cc_final: 0.9165 (mt) REVERT: A 81 MET cc_start: 0.8718 (tpt) cc_final: 0.8481 (tpt) REVERT: A 347 PHE cc_start: 0.8485 (m-80) cc_final: 0.7664 (m-80) outliers start: 4 outliers final: 2 residues processed: 17 average time/residue: 0.2209 time to fit residues: 5.7649 Evaluate side-chains 13 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 376 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 35 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 30 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 overall best weight: 7.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.063747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.045371 restraints weight = 49862.169| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.35 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 9374 Z= 0.391 Angle : 0.690 7.409 13832 Z= 0.354 Chirality : 0.038 0.265 1724 Planarity : 0.004 0.029 870 Dihedral : 26.241 178.229 4135 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.81 % Allowed : 7.77 % Favored : 90.41 % 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: 0.27 (0.42), residues: 429 helix: 1.63 (0.33), residues: 229 sheet: -1.80 (0.52), residues: 86 loop : -1.05 (0.64), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 94 HIS 0.005 0.001 HIS A 370 PHE 0.009 0.002 PHE A 305 TYR 0.012 0.002 TYR A 374 ARG 0.005 0.001 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 11 time to evaluate : 0.556 Fit side-chains REVERT: A 17 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7862 (ttm170) REVERT: A 281 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.7987 (m-80) REVERT: A 564 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8349 (mt-10) outliers start: 7 outliers final: 3 residues processed: 18 average time/residue: 0.2687 time to fit residues: 6.8500 Evaluate side-chains 16 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 10 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 564 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 58 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 6 optimal weight: 30.0000 chunk 12 optimal weight: 0.7980 chunk 50 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.065071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.047097 restraints weight = 48988.939| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.27 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9374 Z= 0.321 Angle : 0.641 7.465 13832 Z= 0.328 Chirality : 0.036 0.273 1724 Planarity : 0.004 0.031 870 Dihedral : 26.086 179.008 4135 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.85 % Allowed : 9.33 % Favored : 87.82 % 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: 0.47 (0.42), residues: 429 helix: 1.80 (0.33), residues: 229 sheet: -1.53 (0.54), residues: 85 loop : -1.18 (0.61), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 94 HIS 0.004 0.001 HIS A 370 PHE 0.012 0.002 PHE A 285 TYR 0.010 0.002 TYR A 474 ARG 0.005 0.001 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 10 time to evaluate : 0.639 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 19 average time/residue: 0.2843 time to fit residues: 7.7467 Evaluate side-chains 16 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 10 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 527 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 54 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 53 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 0.0980 chunk 26 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.069897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.052945 restraints weight = 50042.690| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.09 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9374 Z= 0.144 Angle : 0.568 6.825 13832 Z= 0.285 Chirality : 0.032 0.273 1724 Planarity : 0.004 0.028 870 Dihedral : 25.694 179.899 4135 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.81 % Allowed : 12.18 % Favored : 86.01 % 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: 1.06 (0.42), residues: 429 helix: 2.37 (0.34), residues: 228 sheet: -1.29 (0.52), residues: 84 loop : -1.10 (0.61), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 356 HIS 0.001 0.000 HIS A 586 PHE 0.008 0.001 PHE A 313 TYR 0.008 0.001 TYR A 474 ARG 0.004 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 16 time to evaluate : 0.548 Fit side-chains REVERT: A 353 HIS cc_start: 0.7292 (p90) cc_final: 0.6830 (p90) outliers start: 7 outliers final: 3 residues processed: 22 average time/residue: 0.2108 time to fit residues: 7.1449 Evaluate side-chains 15 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 12 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 368 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 39 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 overall best weight: 9.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN A 496 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.075870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.052362 restraints weight = 55748.580| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.95 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 9374 Z= 0.485 Angle : 0.716 7.389 13832 Z= 0.363 Chirality : 0.040 0.232 1724 Planarity : 0.005 0.029 870 Dihedral : 25.736 177.997 4135 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.37 % Allowed : 12.18 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.42), residues: 429 helix: 1.84 (0.34), residues: 229 sheet: -1.33 (0.54), residues: 83 loop : -1.07 (0.61), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 94 HIS 0.004 0.001 HIS A 370 PHE 0.008 0.002 PHE A 285 TYR 0.016 0.002 TYR A 474 ARG 0.004 0.001 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 11 time to evaluate : 0.580 Fit side-chains REVERT: A 17 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7815 (ttm170) REVERT: A 405 MET cc_start: 0.7570 (ppp) cc_final: 0.6960 (ppp) REVERT: A 570 TYR cc_start: 0.8136 (t80) cc_final: 0.7675 (t80) outliers start: 13 outliers final: 9 residues processed: 22 average time/residue: 0.3264 time to fit residues: 10.3875 Evaluate side-chains 20 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 10 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 608 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 50 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.064502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.046252 restraints weight = 49933.050| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.35 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9374 Z= 0.249 Angle : 0.602 7.028 13832 Z= 0.306 Chirality : 0.034 0.252 1724 Planarity : 0.004 0.030 870 Dihedral : 25.649 178.583 4135 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.11 % Allowed : 12.44 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.42), residues: 429 helix: 2.06 (0.34), residues: 230 sheet: -1.21 (0.53), residues: 84 loop : -1.21 (0.61), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 94 HIS 0.002 0.001 HIS A 522 PHE 0.007 0.001 PHE A 325 TYR 0.014 0.001 TYR A 474 ARG 0.002 0.000 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 12 time to evaluate : 0.720 Fit side-chains REVERT: A 17 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7545 (ttm170) REVERT: A 321 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8663 (pm20) REVERT: A 405 MET cc_start: 0.7839 (ppp) cc_final: 0.7158 (ppp) REVERT: A 570 TYR cc_start: 0.8215 (t80) cc_final: 0.7748 (t80) outliers start: 12 outliers final: 9 residues processed: 22 average time/residue: 0.2556 time to fit residues: 8.2593 Evaluate side-chains 22 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 11 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 608 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 3 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 overall best weight: 9.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.063573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.045388 restraints weight = 50332.960| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.43 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 9374 Z= 0.497 Angle : 0.735 7.159 13832 Z= 0.374 Chirality : 0.040 0.222 1724 Planarity : 0.005 0.032 870 Dihedral : 25.795 179.302 4135 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.15 % Allowed : 11.66 % Favored : 84.20 % 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: 0.27 (0.41), residues: 429 helix: 1.56 (0.33), residues: 230 sheet: -1.39 (0.54), residues: 84 loop : -1.30 (0.59), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 94 HIS 0.004 0.001 HIS A 370 PHE 0.008 0.001 PHE A 325 TYR 0.015 0.002 TYR A 474 ARG 0.004 0.001 ARG A 17 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 10 time to evaluate : 0.721 Fit side-chains REVERT: A 17 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7864 (ttm170) REVERT: A 405 MET cc_start: 0.7859 (ppp) cc_final: 0.7499 (ppp) REVERT: A 570 TYR cc_start: 0.8226 (t80) cc_final: 0.7705 (t80) outliers start: 16 outliers final: 9 residues processed: 26 average time/residue: 0.2926 time to fit residues: 11.2289 Evaluate side-chains 19 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 9 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 608 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 2 optimal weight: 10.0000 chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.065207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.046946 restraints weight = 48767.160| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.26 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9374 Z= 0.207 Angle : 0.608 13.621 13832 Z= 0.304 Chirality : 0.034 0.381 1724 Planarity : 0.004 0.034 870 Dihedral : 25.633 178.664 4135 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.59 % Allowed : 12.95 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.42), residues: 429 helix: 2.03 (0.34), residues: 230 sheet: -1.33 (0.52), residues: 86 loop : -1.26 (0.61), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 588 HIS 0.003 0.001 HIS A 323 PHE 0.008 0.001 PHE A 325 TYR 0.014 0.002 TYR A 474 ARG 0.002 0.000 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 11 time to evaluate : 0.597 Fit side-chains REVERT: A 321 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8665 (pm20) REVERT: A 405 MET cc_start: 0.7822 (ppp) cc_final: 0.7210 (ppp) outliers start: 10 outliers final: 9 residues processed: 19 average time/residue: 0.2228 time to fit residues: 6.5503 Evaluate side-chains 21 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 11 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 608 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 28 optimal weight: 0.1980 chunk 62 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.065062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.046717 restraints weight = 49095.772| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.28 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9374 Z= 0.245 Angle : 0.619 18.441 13832 Z= 0.309 Chirality : 0.035 0.349 1724 Planarity : 0.004 0.034 870 Dihedral : 25.599 179.029 4135 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.85 % Allowed : 12.69 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.42), residues: 429 helix: 2.11 (0.34), residues: 228 sheet: -1.27 (0.51), residues: 86 loop : -1.34 (0.59), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 356 HIS 0.002 0.001 HIS A 370 PHE 0.007 0.001 PHE A 328 TYR 0.013 0.001 TYR A 474 ARG 0.003 0.000 ARG A 300 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 10 time to evaluate : 0.564 Fit side-chains REVERT: A 321 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8598 (pm20) REVERT: A 405 MET cc_start: 0.7836 (ppp) cc_final: 0.7528 (ppp) REVERT: A 551 MET cc_start: 0.8936 (tpp) cc_final: 0.8722 (tpp) outliers start: 11 outliers final: 9 residues processed: 19 average time/residue: 0.2144 time to fit residues: 6.2756 Evaluate side-chains 20 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 10 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 608 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 27 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.064208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.045975 restraints weight = 49718.594| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.34 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9374 Z= 0.289 Angle : 0.629 16.354 13832 Z= 0.315 Chirality : 0.036 0.365 1724 Planarity : 0.004 0.034 870 Dihedral : 25.582 179.549 4135 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.59 % Allowed : 12.69 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.42), residues: 429 helix: 2.05 (0.34), residues: 228 sheet: -1.26 (0.52), residues: 86 loop : -1.34 (0.59), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 94 HIS 0.002 0.001 HIS A 323 PHE 0.007 0.001 PHE A 325 TYR 0.013 0.001 TYR A 474 ARG 0.003 0.000 ARG A 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3996.62 seconds wall clock time: 70 minutes 36.92 seconds (4236.92 seconds total)