Starting phenix.real_space_refine on Sat Dec 28 14:52:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pla_13486/12_2024/7pla_13486_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pla_13486/12_2024/7pla_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_13486/12_2024/7pla_13486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pla_13486/12_2024/7pla_13486.map" model { file = "/net/cci-nas-00/data/ceres_data/7pla_13486/12_2024/7pla_13486_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pla_13486/12_2024/7pla_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-5532/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: 6.17, per 1000 atoms: 0.71 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: 2.70 Conformation dependent library (CDL) restraints added in 454.8 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: 4.83 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: 4.64 Time building geometry restraints manager: 3.01 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: 0.000 Normalize map: mean=0, sd=1: 1.720 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: 0.070 Set scattering table: 0.080 Process input model: 28.550 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.840 ------------------------------------------------------------------------------- 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 : 0.591 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: 0.2848 time to fit residues: 5.5477 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 : 0.477 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5941 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 : 0.639 Fit side-chains REVERT: A 35 LEU cc_start: 0.9280 (mt) cc_final: 0.9027 (mt) REVERT: A 347 PHE cc_start: 0.8337 (m-80) cc_final: 0.7554 (m-80) outliers start: 4 outliers final: 2 residues processed: 17 average time/residue: 0.2478 time to fit residues: 6.5011 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 : 0.663 ------------------------------------------------------------------------------- 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 33 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 59 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9374 Z= 0.391 Angle : 0.693 7.436 13832 Z= 0.356 Chirality : 0.038 0.265 1724 Planarity : 0.005 0.029 870 Dihedral : 26.247 178.143 4135 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.07 % Allowed : 7.77 % Favored : 90.16 % 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: 0.20 (0.41), residues: 429 helix: 1.57 (0.33), residues: 229 sheet: -1.84 (0.51), residues: 86 loop : -1.07 (0.63), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 94 HIS 0.004 0.001 HIS A 370 PHE 0.009 0.002 PHE A 281 TYR 0.014 0.002 TYR A 374 ARG 0.004 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: 8 poor density : 10 time to evaluate : 0.605 Fit side-chains REVERT: A 35 LEU cc_start: 0.9324 (mt) cc_final: 0.9075 (mt) REVERT: A 281 PHE cc_start: 0.7837 (OUTLIER) cc_final: 0.7456 (m-80) outliers start: 8 outliers final: 4 residues processed: 18 average time/residue: 0.2743 time to fit residues: 7.1837 Evaluate side-chains 15 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 10 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 312 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 31 optimal weight: 30.0000 chunk 6 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 53 optimal weight: 20.0000 overall best weight: 5.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN A 415 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5987 moved from start: 0.3188 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= 0.318 Angle : 0.640 7.227 13832 Z= 0.327 Chirality : 0.036 0.267 1724 Planarity : 0.004 0.030 870 Dihedral : 26.012 178.961 4135 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.30 % Allowed : 9.84 % Favored : 88.86 % 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: 1.75 (0.33), residues: 229 sheet: -1.50 (0.53), residues: 84 loop : -1.07 (0.62), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 94 HIS 0.003 0.001 HIS A 370 PHE 0.010 0.002 PHE A 285 TYR 0.010 0.002 TYR A 374 ARG 0.009 0.001 ARG A 17 *********************** 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 16 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 11 time to evaluate : 0.616 Fit side-chains REVERT: A 35 LEU cc_start: 0.9372 (mt) cc_final: 0.9138 (mt) REVERT: A 405 MET cc_start: 0.7911 (ppp) cc_final: 0.7559 (ppp) outliers start: 5 outliers final: 1 residues processed: 16 average time/residue: 0.3130 time to fit residues: 7.2216 Evaluate side-chains 12 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 11 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 chunk 16 optimal weight: 0.4980 chunk 21 optimal weight: 20.0000 chunk 12 optimal weight: 0.7980 overall best weight: 2.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5897 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9374 Z= 0.191 Angle : 0.574 6.979 13832 Z= 0.290 Chirality : 0.033 0.262 1724 Planarity : 0.004 0.029 870 Dihedral : 25.719 179.071 4135 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.11 % Allowed : 9.84 % Favored : 87.05 % 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: 2.07 (0.34), residues: 230 sheet: -1.33 (0.52), residues: 84 loop : -1.16 (0.61), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 94 HIS 0.001 0.000 HIS A 323 PHE 0.008 0.001 PHE A 313 TYR 0.010 0.001 TYR A 474 ARG 0.005 0.000 ARG A 17 *********************** 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 26 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 14 time to evaluate : 0.581 Fit side-chains REVERT: A 35 LEU cc_start: 0.9381 (mt) cc_final: 0.9137 (mt) REVERT: A 281 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.7536 (m-80) REVERT: A 405 MET cc_start: 0.8025 (ppp) cc_final: 0.7791 (ppp) REVERT: A 551 MET cc_start: 0.8865 (mmm) cc_final: 0.8634 (tpp) outliers start: 12 outliers final: 8 residues processed: 23 average time/residue: 0.2059 time to fit residues: 7.3328 Evaluate side-chains 20 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 11 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 291 MET 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 608 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 7 optimal weight: 30.0000 chunk 36 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5979 moved from start: 0.3664 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= 0.323 Angle : 0.626 6.956 13832 Z= 0.319 Chirality : 0.035 0.239 1724 Planarity : 0.004 0.029 870 Dihedral : 25.681 178.029 4135 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.63 % Allowed : 10.88 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.42), residues: 429 helix: 2.03 (0.34), residues: 227 sheet: -1.26 (0.54), residues: 83 loop : -1.13 (0.60), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 94 HIS 0.003 0.001 HIS A 370 PHE 0.010 0.002 PHE A 285 TYR 0.015 0.002 TYR A 474 ARG 0.006 0.001 ARG A 17 *********************** 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 27 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 13 time to evaluate : 0.605 Fit side-chains REVERT: A 281 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.7543 (m-80) REVERT: A 570 TYR cc_start: 0.8151 (t80) cc_final: 0.7778 (t80) outliers start: 14 outliers final: 9 residues processed: 24 average time/residue: 0.2078 time to fit residues: 7.7589 Evaluate side-chains 22 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 12 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 288 ASN Chi-restraints excluded: chain A residue 291 MET 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 608 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 19 optimal weight: 30.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5894 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9374 Z= 0.185 Angle : 0.573 8.643 13832 Z= 0.289 Chirality : 0.032 0.251 1724 Planarity : 0.004 0.030 870 Dihedral : 25.560 178.622 4135 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.33 % Allowed : 12.18 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.42), residues: 429 helix: 2.25 (0.34), residues: 227 sheet: -1.10 (0.52), residues: 84 loop : -1.20 (0.60), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 588 HIS 0.002 0.001 HIS A 304 PHE 0.008 0.001 PHE A 313 TYR 0.013 0.001 TYR A 474 ARG 0.004 0.000 ARG A 17 *********************** 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 22 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 13 time to evaluate : 0.619 Fit side-chains REVERT: A 281 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7697 (m-80) outliers start: 9 outliers final: 7 residues processed: 20 average time/residue: 0.2171 time to fit residues: 6.6645 Evaluate side-chains 20 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 12 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 291 MET 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 608 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 overall best weight: 5.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5977 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9374 Z= 0.328 Angle : 0.647 11.529 13832 Z= 0.326 Chirality : 0.036 0.327 1724 Planarity : 0.004 0.029 870 Dihedral : 25.593 178.304 4135 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.85 % Allowed : 12.44 % 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: 0.72 (0.42), residues: 429 helix: 2.06 (0.34), residues: 227 sheet: -1.23 (0.52), residues: 84 loop : -1.31 (0.59), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 94 HIS 0.003 0.001 HIS A 370 PHE 0.008 0.002 PHE A 281 TYR 0.015 0.002 TYR A 474 ARG 0.006 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 23 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 12 time to evaluate : 0.608 Fit side-chains REVERT: A 281 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7605 (m-80) REVERT: A 405 MET cc_start: 0.7950 (ppp) cc_final: 0.7430 (ppp) REVERT: A 570 TYR cc_start: 0.8157 (t80) cc_final: 0.7774 (t80) outliers start: 11 outliers final: 9 residues processed: 21 average time/residue: 0.2158 time to fit residues: 6.9832 Evaluate side-chains 22 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 12 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 291 MET 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 608 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 overall best weight: 4.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5938 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9374 Z= 0.256 Angle : 0.617 16.220 13832 Z= 0.307 Chirality : 0.035 0.377 1724 Planarity : 0.004 0.030 870 Dihedral : 25.561 179.059 4135 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.11 % Allowed : 12.18 % 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: 0.77 (0.42), residues: 429 helix: 2.13 (0.34), residues: 227 sheet: -1.24 (0.50), residues: 86 loop : -1.34 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 588 HIS 0.002 0.001 HIS A 323 PHE 0.009 0.001 PHE A 313 TYR 0.013 0.001 TYR A 474 ARG 0.005 0.000 ARG A 17 *********************** 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 24 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 12 time to evaluate : 0.623 Fit side-chains REVERT: A 281 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7617 (m-80) REVERT: A 405 MET cc_start: 0.7965 (ppp) cc_final: 0.7472 (ppp) outliers start: 12 outliers final: 9 residues processed: 21 average time/residue: 0.2159 time to fit residues: 7.0855 Evaluate side-chains 22 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 12 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 288 ASN Chi-restraints excluded: chain A residue 291 MET 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 608 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 5 optimal weight: 30.0000 chunk 40 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 16 optimal weight: 0.0970 chunk 48 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 overall best weight: 4.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5942 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9374 Z= 0.256 Angle : 0.616 16.779 13832 Z= 0.307 Chirality : 0.035 0.368 1724 Planarity : 0.004 0.030 870 Dihedral : 25.551 179.547 4135 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.85 % Allowed : 12.18 % Favored : 84.97 % 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: 0.76 (0.41), residues: 429 helix: 2.16 (0.34), residues: 228 sheet: -1.28 (0.51), residues: 86 loop : -1.42 (0.58), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 94 HIS 0.002 0.001 HIS A 370 PHE 0.008 0.001 PHE A 313 TYR 0.013 0.001 TYR A 474 ARG 0.005 0.001 ARG A 17 ********************** 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 23 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 12 time to evaluate : 0.702 Fit side-chains REVERT: A 281 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.7664 (m-80) REVERT: A 405 MET cc_start: 0.7985 (ppp) cc_final: 0.7503 (ppp) outliers start: 11 outliers final: 9 residues processed: 21 average time/residue: 0.2108 time to fit residues: 6.9892 Evaluate side-chains 22 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 12 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 288 ASN Chi-restraints excluded: chain A residue 291 MET 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 608 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 20.0000 chunk 21 optimal weight: 30.0000 chunk 53 optimal weight: 20.0000 chunk 6 optimal weight: 30.0000 chunk 9 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.063434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.045002 restraints weight = 49211.802| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.38 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 9374 Z= 0.419 Angle : 0.696 16.557 13832 Z= 0.349 Chirality : 0.038 0.355 1724 Planarity : 0.004 0.031 870 Dihedral : 25.643 179.281 4135 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.85 % Allowed : 11.92 % Favored : 85.23 % 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: 0.45 (0.42), residues: 429 helix: 1.83 (0.34), residues: 228 sheet: -1.39 (0.53), residues: 88 loop : -1.39 (0.60), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 94 HIS 0.004 0.001 HIS A 370 PHE 0.009 0.001 PHE A 281 TYR 0.014 0.002 TYR A 474 ARG 0.005 0.001 ARG A 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1252.95 seconds wall clock time: 24 minutes 32.18 seconds (1472.18 seconds total)