Starting phenix.real_space_refine on Mon Mar 11 16:33:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pla_13486/03_2024/7pla_13486_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pla_13486/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pla_13486/03_2024/7pla_13486.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pla_13486/03_2024/7pla_13486.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pla_13486/03_2024/7pla_13486_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pla_13486/03_2024/7pla_13486_neut.pdb" } 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 Residue "A TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 410": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.71, 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 - 3.50 Amino acid : False - 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: 4.97 Conformation dependent library (CDL) restraints added in 655.6 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: 4.51 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: 3.88 Time building geometry restraints manager: 5.07 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: 98.34 - 105.51: 1168 105.51 - 112.68: 5242 112.68 - 119.85: 3546 119.85 - 127.02: 3280 127.02 - 134.19: 596 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 2.520 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 2.440 nonbonded pdb=" O TRP A 293 " pdb=" NE2 GLN A 332 " model vdw 2.258 2.520 nonbonded pdb=" NZ LYS A 547 " pdb=" OE1 GLU A 610 " model vdw 2.284 2.520 ... (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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.960 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: 6.040 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 31.610 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.630 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.601 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: 0.2846 time to fit residues: 5.4430 Evaluate side-chains 11 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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: 5.9990 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 20 optimal weight: 30.0000 chunk 31 optimal weight: 30.0000 chunk 38 optimal weight: 0.9990 chunk 59 optimal weight: 20.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5915 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9374 Z= 0.242 Angle : 0.654 7.281 13832 Z= 0.338 Chirality : 0.037 0.267 1724 Planarity : 0.004 0.031 870 Dihedral : 26.565 179.160 4135 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.04 % Allowed : 4.40 % Favored : 94.56 % 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: 0.53 (0.41), residues: 429 helix: 1.72 (0.33), residues: 232 sheet: -1.13 (0.60), residues: 69 loop : -1.31 (0.56), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 94 HIS 0.003 0.001 HIS A 522 PHE 0.009 0.001 PHE A 313 TYR 0.010 0.001 TYR A 80 ARG 0.003 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 17 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 13 time to evaluate : 0.594 Fit side-chains REVERT: A 35 LEU cc_start: 0.9277 (mt) cc_final: 0.9022 (mt) REVERT: A 347 PHE cc_start: 0.8272 (m-80) cc_final: 0.7598 (m-80) outliers start: 4 outliers final: 2 residues processed: 16 average time/residue: 0.2394 time to fit residues: 5.8730 Evaluate side-chains 13 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 11 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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: 1.9990 chunk 18 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 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: 10.0000 chunk 48 optimal weight: 10.0000 overall best weight: 7.3996 ------------------------------------------------------------------------------- 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: 0.6023 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9374 Z= 0.393 Angle : 0.686 7.485 13832 Z= 0.352 Chirality : 0.039 0.270 1724 Planarity : 0.005 0.034 870 Dihedral : 26.235 176.791 4135 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % 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: 0.21 (0.41), residues: 429 helix: 1.66 (0.33), residues: 229 sheet: -1.79 (0.52), residues: 85 loop : -1.30 (0.60), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 94 HIS 0.005 0.001 HIS A 370 PHE 0.010 0.002 PHE A 305 TYR 0.013 0.002 TYR A 374 ARG 0.004 0.001 ARG A 380 *********************** 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 fitting. rotamer outliers: 7 poor density : 11 time to evaluate : 1.299 Fit side-chains REVERT: A 35 LEU cc_start: 0.9321 (mt) cc_final: 0.9068 (mt) REVERT: A 281 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.7450 (m-80) REVERT: A 564 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8307 (mt-10) outliers start: 7 outliers final: 3 residues processed: 18 average time/residue: 0.3702 time to fit residues: 10.1562 Evaluate side-chains 14 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 9 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 59 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 31 optimal weight: 30.0000 chunk 6 optimal weight: 30.0000 chunk 28 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 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: 6.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6007 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9374 Z= 0.357 Angle : 0.651 7.269 13832 Z= 0.333 Chirality : 0.037 0.261 1724 Planarity : 0.004 0.031 870 Dihedral : 26.052 177.987 4135 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.59 % Allowed : 8.29 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.41), residues: 429 helix: 1.67 (0.34), residues: 229 sheet: -1.75 (0.51), residues: 85 loop : -1.37 (0.59), residues: 115 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 0.010 0.002 PHE A 281 TYR 0.010 0.002 TYR A 374 ARG 0.007 0.001 ARG A 78 *********************** 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 20 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 10 time to evaluate : 0.588 Fit side-chains REVERT: A 35 LEU cc_start: 0.9382 (mt) cc_final: 0.9125 (mt) outliers start: 10 outliers final: 5 residues processed: 19 average time/residue: 0.2691 time to fit residues: 7.3289 Evaluate side-chains 16 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 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 284 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 376 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 16 optimal weight: 0.1980 chunk 21 optimal weight: 50.0000 chunk 12 optimal weight: 3.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 GLN A 496 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5881 moved from start: 0.3600 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= 0.173 Angle : 0.568 7.827 13832 Z= 0.286 Chirality : 0.032 0.265 1724 Planarity : 0.004 0.029 870 Dihedral : 25.733 179.178 4135 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.33 % Allowed : 9.33 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.41), residues: 429 helix: 2.18 (0.34), residues: 228 sheet: -1.38 (0.51), residues: 84 loop : -1.26 (0.58), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 94 HIS 0.001 0.000 HIS A 85 PHE 0.019 0.001 PHE A 285 TYR 0.009 0.001 TYR A 474 ARG 0.002 0.000 ARG A 435 *********************** 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 fitting. rotamer outliers: 9 poor density : 14 time to evaluate : 0.602 Fit side-chains REVERT: A 17 ARG cc_start: 0.5942 (OUTLIER) cc_final: 0.5009 (mtm180) REVERT: A 35 LEU cc_start: 0.9388 (mt) cc_final: 0.9145 (mt) REVERT: A 281 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7525 (m-80) REVERT: A 405 MET cc_start: 0.7867 (ppp) cc_final: 0.6945 (ppp) REVERT: A 551 MET cc_start: 0.8813 (mmm) cc_final: 0.8612 (tpp) outliers start: 9 outliers final: 4 residues processed: 23 average time/residue: 0.2697 time to fit residues: 8.8551 Evaluate side-chains 20 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 14 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 344 SER 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: 20.0000 chunk 63 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 chunk 21 optimal weight: 50.0000 chunk 33 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 7 optimal weight: 30.0000 chunk 36 optimal weight: 6.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- 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: 0.5948 moved from start: 0.3661 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= 0.275 Angle : 0.593 7.189 13832 Z= 0.302 Chirality : 0.034 0.245 1724 Planarity : 0.004 0.030 870 Dihedral : 25.696 178.239 4135 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.89 % Allowed : 9.84 % Favored : 86.27 % 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: 2.06 (0.34), residues: 230 sheet: -1.23 (0.52), residues: 82 loop : -1.30 (0.57), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 94 HIS 0.003 0.001 HIS A 323 PHE 0.008 0.001 PHE A 313 TYR 0.015 0.001 TYR A 474 ARG 0.003 0.001 ARG A 78 *********************** 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 fitting. rotamer outliers: 15 poor density : 12 time to evaluate : 0.578 Fit side-chains REVERT: A 17 ARG cc_start: 0.6115 (OUTLIER) cc_final: 0.5541 (mtm180) REVERT: A 281 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.7538 (m-80) REVERT: A 405 MET cc_start: 0.7965 (ppp) cc_final: 0.7088 (ppp) outliers start: 15 outliers final: 9 residues processed: 25 average time/residue: 0.2389 time to fit residues: 8.6102 Evaluate side-chains 22 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 11 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 81 MET 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 321 GLN Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 527 LEU 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: 10.0000 chunk 53 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 19 optimal weight: 30.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5876 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9374 Z= 0.168 Angle : 0.563 11.923 13832 Z= 0.281 Chirality : 0.032 0.253 1724 Planarity : 0.004 0.030 870 Dihedral : 25.609 178.448 4135 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.85 % Allowed : 11.66 % 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: 0.95 (0.42), residues: 429 helix: 2.29 (0.34), residues: 229 sheet: -1.09 (0.50), residues: 83 loop : -1.41 (0.57), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 588 HIS 0.002 0.001 HIS A 369 PHE 0.008 0.001 PHE A 313 TYR 0.012 0.001 TYR A 474 ARG 0.002 0.000 ARG A 435 *********************** 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 26 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 15 time to evaluate : 0.560 Fit side-chains REVERT: A 17 ARG cc_start: 0.5954 (OUTLIER) cc_final: 0.5069 (mtm180) REVERT: A 281 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.7673 (m-80) REVERT: A 405 MET cc_start: 0.7962 (ppp) cc_final: 0.7681 (ppp) outliers start: 11 outliers final: 6 residues processed: 24 average time/residue: 0.2381 time to fit residues: 8.2824 Evaluate side-chains 20 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 12 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 312 ILE Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 376 CYS 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: 4.9990 chunk 40 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 31 optimal weight: 0.0770 chunk 5 optimal weight: 0.5980 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: 7.9990 overall best weight: 4.1344 ------------------------------------------------------------------------------- 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: 0.5921 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9374 Z= 0.239 Angle : 0.583 11.584 13832 Z= 0.294 Chirality : 0.034 0.338 1724 Planarity : 0.004 0.029 870 Dihedral : 25.595 177.932 4135 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.37 % Allowed : 11.92 % 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: 0.91 (0.41), residues: 429 helix: 2.21 (0.34), residues: 230 sheet: -1.12 (0.52), residues: 84 loop : -1.34 (0.58), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 94 HIS 0.003 0.001 HIS A 370 PHE 0.008 0.001 PHE A 313 TYR 0.014 0.001 TYR A 474 ARG 0.002 0.000 ARG A 492 *********************** 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 fitting. rotamer outliers: 13 poor density : 13 time to evaluate : 0.616 Fit side-chains REVERT: A 281 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7644 (m-80) REVERT: A 405 MET cc_start: 0.7963 (ppp) cc_final: 0.7715 (ppp) outliers start: 13 outliers final: 10 residues processed: 23 average time/residue: 0.2591 time to fit residues: 8.5114 Evaluate side-chains 24 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 13 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 321 GLN Chi-restraints excluded: chain A residue 344 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 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: 6.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6001 moved from start: 0.3974 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= 0.367 Angle : 0.662 15.798 13832 Z= 0.333 Chirality : 0.037 0.384 1724 Planarity : 0.004 0.030 870 Dihedral : 25.712 178.328 4135 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.37 % Allowed : 11.40 % 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: 0.51 (0.41), residues: 429 helix: 1.83 (0.34), residues: 228 sheet: -1.22 (0.52), residues: 85 loop : -1.38 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 21 HIS 0.004 0.001 HIS A 370 PHE 0.010 0.002 PHE A 313 TYR 0.014 0.002 TYR A 474 ARG 0.003 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 26 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 13 time to evaluate : 0.598 Fit side-chains REVERT: A 281 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7581 (m-80) REVERT: A 405 MET cc_start: 0.7974 (ppp) cc_final: 0.7741 (ppp) REVERT: A 570 TYR cc_start: 0.8164 (t80) cc_final: 0.7794 (t80) outliers start: 13 outliers final: 8 residues processed: 24 average time/residue: 0.2449 time to fit residues: 8.4833 Evaluate side-chains 22 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 13 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 312 ILE Chi-restraints excluded: chain A residue 344 SER 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: 5.9990 chunk 40 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 7 optimal weight: 30.0000 chunk 14 optimal weight: 7.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5904 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9374 Z= 0.202 Angle : 0.588 16.624 13832 Z= 0.292 Chirality : 0.034 0.389 1724 Planarity : 0.004 0.031 870 Dihedral : 25.587 178.931 4135 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.33 % Allowed : 12.44 % 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: 0.81 (0.41), residues: 429 helix: 2.07 (0.34), residues: 227 sheet: -0.92 (0.51), residues: 84 loop : -1.38 (0.57), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 356 HIS 0.002 0.001 HIS A 323 PHE 0.010 0.001 PHE A 313 TYR 0.012 0.001 TYR A 474 ARG 0.002 0.000 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 22 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 13 time to evaluate : 0.591 Fit side-chains REVERT: A 281 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7635 (m-80) REVERT: A 405 MET cc_start: 0.7965 (ppp) cc_final: 0.7732 (ppp) outliers start: 9 outliers final: 7 residues processed: 21 average time/residue: 0.2571 time to fit residues: 7.8690 Evaluate side-chains 20 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 12 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 312 ILE Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 376 CYS 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: 8.9990 chunk 53 optimal weight: 20.0000 chunk 6 optimal weight: 40.0000 chunk 9 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 overall best weight: 9.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.063411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.045155 restraints weight = 49480.042| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.42 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 9374 Z= 0.468 Angle : 0.716 16.287 13832 Z= 0.360 Chirality : 0.040 0.355 1724 Planarity : 0.005 0.059 870 Dihedral : 25.731 179.409 4135 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.07 % Allowed : 12.69 % 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: 0.15 (0.40), residues: 429 helix: 1.49 (0.33), residues: 227 sheet: -1.28 (0.51), residues: 85 loop : -1.49 (0.57), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 21 HIS 0.005 0.001 HIS A 370 PHE 0.010 0.002 PHE A 281 TYR 0.012 0.002 TYR A 474 ARG 0.012 0.001 ARG A 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1287.18 seconds wall clock time: 24 minutes 52.42 seconds (1492.42 seconds total)