Starting phenix.real_space_refine on Sun Mar 10 16:44:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8goe_34176/03_2024/8goe_34176_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8goe_34176/03_2024/8goe_34176.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8goe_34176/03_2024/8goe_34176_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8goe_34176/03_2024/8goe_34176_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8goe_34176/03_2024/8goe_34176_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8goe_34176/03_2024/8goe_34176.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8goe_34176/03_2024/8goe_34176.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8goe_34176/03_2024/8goe_34176_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8goe_34176/03_2024/8goe_34176_neut_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 2204 2.51 5 N 555 2.21 5 O 554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 26": "NH1" <-> "NH2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A ARG 179": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ARG 303": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A ARG 333": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3323 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3323 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3301 Unusual residues: {'THH': 1} Classifications: {'peptide': 407, 'undetermined': 1} Link IDs: {'PTRANS': 14, 'TRANS': 392, None: 1} Not linked: pdbres="HIS A 457 " pdbres="THH A 601 " Chain breaks: 1 Conformer: "B" Number of residues, atoms: 408, 3299 Unusual residues: {'THH': 1} Classifications: {'peptide': 407, 'undetermined': 1} Link IDs: {'PTRANS': 14, 'TRANS': 392, None: 1} Not linked: pdbres="HIS A 457 " pdbres="THH A 601 " Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen planarities: 2 bond proxies already assigned to first conformer: 3364 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 133 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 133 " occ=0.50 residue: pdb=" N AARG A 208 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 208 " occ=0.50 Time building chain proxies: 3.88, per 1000 atoms: 1.17 Number of scatterers: 3323 At special positions: 0 Unit cell: (78, 73, 67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 554 8.00 N 555 7.00 C 2204 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: 1.38 Conformation dependent library (CDL) restraints added in 1.3 seconds 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB THH A 601 " Number of C-beta restraints generated: 774 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 0 sheets defined 72.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 26 through 40 removed outlier: 3.754A pdb=" N TYR A 31 " --> pdb=" O HIS A 27 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE A 34 " --> pdb=" O CYS A 30 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 37 " --> pdb=" O CYS A 33 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLN A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 52 No H-bonds generated for 'chain 'A' and resid 49 through 52' Processing helix chain 'A' and resid 61 through 64 No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 69 through 89 removed outlier: 3.959A pdb=" N SER A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 3.662A pdb=" N ASP A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 112 removed outlier: 3.559A pdb=" N LEU A 111 " --> pdb=" O TRP A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 131 removed outlier: 3.596A pdb=" N THR A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 removed outlier: 3.955A pdb=" N TYR A 136 " --> pdb=" O AARG A 133 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A 137 " --> pdb=" O ILE A 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 133 through 137' Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 149 through 175 removed outlier: 3.586A pdb=" N LEU A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 201 Processing helix chain 'A' and resid 250 through 256 Processing helix chain 'A' and resid 259 through 262 No H-bonds generated for 'chain 'A' and resid 259 through 262' Processing helix chain 'A' and resid 267 through 276 removed outlier: 3.741A pdb=" N LEU A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.552A pdb=" N VAL A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 295 Processing helix chain 'A' and resid 301 through 303 No H-bonds generated for 'chain 'A' and resid 301 through 303' Processing helix chain 'A' and resid 306 through 324 removed outlier: 3.624A pdb=" N SER A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 355 Processing helix chain 'A' and resid 359 through 387 removed outlier: 3.567A pdb=" N ILE A 362 " --> pdb=" O PRO A 359 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TRP A 363 " --> pdb=" O SER A 360 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A 368 " --> pdb=" O CYS A 365 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 370 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LEU A 371 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY A 374 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR A 376 " --> pdb=" O ARG A 373 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN A 377 " --> pdb=" O GLY A 374 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 378 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A 380 " --> pdb=" O GLN A 377 " (cutoff:3.500A) Proline residue: A 381 - end of helix removed outlier: 3.751A pdb=" N THR A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 385 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN A 386 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A 387 " --> pdb=" O THR A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 417 Processing helix chain 'A' and resid 428 through 452 removed outlier: 3.607A pdb=" N LEU A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) 174 hydrogen bonds defined for protein. 498 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.96 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 472 1.31 - 1.43: 1057 1.43 - 1.56: 1871 1.56 - 1.68: 1 1.68 - 1.81: 16 Bond restraints: 3417 Sorted by residual: bond pdb=" C4 THH A 601 " pdb=" O4 THH A 601 " ideal model delta sigma weight residual 1.401 1.184 0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" N LEU A 121 " pdb=" CA LEU A 121 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.21e-02 6.83e+03 5.52e+00 bond pdb=" N MET A 122 " pdb=" CA MET A 122 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.18e+00 bond pdb=" N GLU A 123 " pdb=" CA GLU A 123 " ideal model delta sigma weight residual 1.459 1.487 -0.029 1.28e-02 6.10e+03 5.09e+00 bond pdb=" N GLN A 120 " pdb=" CA GLN A 120 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.23e-02 6.61e+03 4.26e+00 ... (remaining 3412 not shown) Histogram of bond angle deviations from ideal: 99.56 - 106.46: 80 106.46 - 113.35: 1838 113.35 - 120.25: 1401 120.25 - 127.14: 1299 127.14 - 134.03: 41 Bond angle restraints: 4659 Sorted by residual: angle pdb=" C TYR A 92 " pdb=" CA TYR A 92 " pdb=" CB TYR A 92 " ideal model delta sigma weight residual 111.23 101.44 9.79 1.63e+00 3.76e-01 3.60e+01 angle pdb=" N GLN A 120 " pdb=" CA GLN A 120 " pdb=" C GLN A 120 " ideal model delta sigma weight residual 111.36 105.80 5.56 1.09e+00 8.42e-01 2.60e+01 angle pdb=" CA VAL A 327 " pdb=" CB VAL A 327 " pdb=" CG1 VAL A 327 " ideal model delta sigma weight residual 110.40 115.30 -4.90 1.70e+00 3.46e-01 8.30e+00 angle pdb=" N THR A 69 " pdb=" CA THR A 69 " pdb=" C THR A 69 " ideal model delta sigma weight residual 109.81 115.98 -6.17 2.21e+00 2.05e-01 7.79e+00 angle pdb=" CA THR A 49 " pdb=" C THR A 49 " pdb=" N PRO A 50 " ideal model delta sigma weight residual 118.44 122.66 -4.22 1.59e+00 3.96e-01 7.06e+00 ... (remaining 4654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.43: 1826 18.43 - 36.86: 107 36.86 - 55.30: 26 55.30 - 73.73: 4 73.73 - 92.16: 2 Dihedral angle restraints: 1965 sinusoidal: 759 harmonic: 1206 Sorted by residual: dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 154.86 25.14 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA LEU A 452 " pdb=" C LEU A 452 " pdb=" N ASP A 453 " pdb=" CA ASP A 453 " ideal model delta harmonic sigma weight residual 180.00 161.97 18.03 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" C7 THH A 601 " pdb=" C6 THH A 601 " pdb=" N5 THH A 601 " pdb=" C4AATHH A 601 " ideal model delta sinusoidal sigma weight residual -38.23 53.93 -92.16 1 3.00e+01 1.11e-03 1.11e+01 ... (remaining 1962 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 345 0.039 - 0.077: 152 0.077 - 0.116: 29 0.116 - 0.155: 7 0.155 - 0.193: 4 Chirality restraints: 537 Sorted by residual: chirality pdb=" CA ARG A 42 " pdb=" N ARG A 42 " pdb=" C ARG A 42 " pdb=" CB ARG A 42 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.34e-01 chirality pdb=" CA LEU A 121 " pdb=" N LEU A 121 " pdb=" C LEU A 121 " pdb=" CB LEU A 121 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CA MET A 122 " pdb=" N MET A 122 " pdb=" C MET A 122 " pdb=" CB MET A 122 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.17 2.00e-01 2.50e+01 7.65e-01 ... (remaining 534 not shown) Planarity restraints: 566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 69 " 0.041 5.00e-02 4.00e+02 6.10e-02 5.96e+00 pdb=" N PRO A 70 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 41 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" C ILE A 41 " -0.036 2.00e-02 2.50e+03 pdb=" O ILE A 41 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG A 42 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 81 " -0.035 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO A 82 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " -0.030 5.00e-02 4.00e+02 ... (remaining 563 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1003 2.80 - 3.32: 3020 3.32 - 3.85: 5714 3.85 - 4.37: 7164 4.37 - 4.90: 11743 Nonbonded interactions: 28644 Sorted by model distance: nonbonded pdb=" NH2 ARG A 42 " pdb=" OE2 GLU A 45 " model vdw 2.273 2.520 nonbonded pdb=" O VAL A 304 " pdb=" OH TYR A 366 " model vdw 2.286 2.440 nonbonded pdb=" O VAL A 64 " pdb=" OG1 THR A 69 " model vdw 2.296 2.440 nonbonded pdb=" O LEU A 32 " pdb=" OH TYR A 136 " model vdw 2.301 2.440 nonbonded pdb=" OE2 GLU A 45 " pdb=" OH TYR A 126 " model vdw 2.313 2.440 ... (remaining 28639 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=0.50 max=1.00 mean=0.99 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.030 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.490 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:14.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 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 : 0.006 0.217 3417 Z= 0.375 Angle : 0.764 9.785 4659 Z= 0.451 Chirality : 0.046 0.193 537 Planarity : 0.006 0.061 566 Dihedral : 13.251 92.160 1191 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.57 % Allowed : 8.50 % Favored : 90.93 % Cbeta Deviations : 0.26 % 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: -6.19 (0.23), residues: 409 helix: -4.26 (0.12), residues: 323 sheet: None (None), residues: 0 loop : -2.02 (0.53), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.002 0.001 HIS A 358 PHE 0.010 0.002 PHE A 37 TYR 0.008 0.001 TYR A 92 ARG 0.004 0.001 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.384 Fit side-chains REVERT: A 88 ASP cc_start: 0.8379 (t70) cc_final: 0.8063 (t70) REVERT: A 294 GLU cc_start: 0.8068 (tt0) cc_final: 0.7688 (tt0) REVERT: A 445 ILE cc_start: 0.8561 (mt) cc_final: 0.8268 (mt) REVERT: A 452 LEU cc_start: 0.7280 (mt) cc_final: 0.7038 (mt) outliers start: 2 outliers final: 1 residues processed: 54 average time/residue: 1.0379 time to fit residues: 58.0931 Evaluate side-chains 36 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.5980 chunk 30 optimal weight: 0.1980 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 266 GLN A 277 ASN A 377 GLN A 431 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3417 Z= 0.189 Angle : 0.545 8.974 4659 Z= 0.276 Chirality : 0.037 0.103 537 Planarity : 0.005 0.036 566 Dihedral : 8.571 78.472 475 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.85 % Allowed : 10.48 % Favored : 88.67 % Cbeta Deviations : 0.26 % 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: -3.02 (0.32), residues: 409 helix: -1.87 (0.23), residues: 317 sheet: None (None), residues: 0 loop : -1.65 (0.52), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.009 0.001 PHE A 372 TYR 0.009 0.001 TYR A 149 ARG 0.003 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 161 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.6981 (mm) REVERT: A 294 GLU cc_start: 0.8045 (tt0) cc_final: 0.7548 (tt0) REVERT: A 452 LEU cc_start: 0.7189 (mt) cc_final: 0.6985 (mt) outliers start: 3 outliers final: 0 residues processed: 37 average time/residue: 0.9364 time to fit residues: 36.2982 Evaluate side-chains 36 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3417 Z= 0.231 Angle : 0.532 7.866 4659 Z= 0.264 Chirality : 0.038 0.112 537 Planarity : 0.004 0.030 566 Dihedral : 8.159 72.355 474 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.13 % Allowed : 11.05 % Favored : 87.82 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.38), residues: 409 helix: -0.50 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.26 (0.56), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.026 0.001 PHE A 322 TYR 0.011 0.001 TYR A 149 ARG 0.003 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.433 Fit side-chains REVERT: A 161 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7275 (mp) REVERT: A 294 GLU cc_start: 0.8121 (tt0) cc_final: 0.7629 (tt0) outliers start: 4 outliers final: 2 residues processed: 40 average time/residue: 0.9984 time to fit residues: 41.7060 Evaluate side-chains 40 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 251 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 0.0020 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3417 Z= 0.183 Angle : 0.513 9.393 4659 Z= 0.249 Chirality : 0.038 0.107 537 Planarity : 0.003 0.027 566 Dihedral : 7.802 67.560 474 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.85 % Allowed : 11.90 % Favored : 87.25 % Cbeta Deviations : 0.26 % 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: -0.35 (0.39), residues: 409 helix: 0.09 (0.28), residues: 320 sheet: None (None), residues: 0 loop : -0.99 (0.56), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.007 0.001 PHE A 372 TYR 0.009 0.001 TYR A 149 ARG 0.002 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.404 Fit side-chains REVERT: A 161 LEU cc_start: 0.7524 (pp) cc_final: 0.7302 (mp) REVERT: A 294 GLU cc_start: 0.8114 (tt0) cc_final: 0.7609 (tt0) outliers start: 3 outliers final: 3 residues processed: 41 average time/residue: 0.8074 time to fit residues: 34.7208 Evaluate side-chains 37 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.0670 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3417 Z= 0.185 Angle : 0.510 9.148 4659 Z= 0.249 Chirality : 0.038 0.116 537 Planarity : 0.003 0.026 566 Dihedral : 7.626 64.598 474 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.13 % Allowed : 12.46 % Favored : 86.40 % Cbeta Deviations : 0.26 % 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: 0.04 (0.40), residues: 409 helix: 0.37 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -0.84 (0.58), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.027 0.001 PHE A 322 TYR 0.010 0.001 TYR A 149 ARG 0.002 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.384 Fit side-chains REVERT: A 161 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7213 (mp) REVERT: A 294 GLU cc_start: 0.8168 (tt0) cc_final: 0.7649 (tt0) outliers start: 4 outliers final: 2 residues processed: 38 average time/residue: 1.0171 time to fit residues: 40.4496 Evaluate side-chains 37 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.0170 chunk 28 optimal weight: 0.9980 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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: 0.7814 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3417 Z= 0.183 Angle : 0.513 10.179 4659 Z= 0.248 Chirality : 0.038 0.126 537 Planarity : 0.003 0.025 566 Dihedral : 7.516 62.788 474 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.70 % Allowed : 11.90 % Favored : 86.40 % Cbeta Deviations : 0.26 % 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: 0.30 (0.40), residues: 409 helix: 0.54 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -0.70 (0.59), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.007 0.001 PHE A 372 TYR 0.009 0.001 TYR A 149 ARG 0.002 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 161 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7208 (mp) REVERT: A 294 GLU cc_start: 0.8160 (tt0) cc_final: 0.7641 (tt0) outliers start: 6 outliers final: 4 residues processed: 39 average time/residue: 0.9494 time to fit residues: 38.7203 Evaluate side-chains 40 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.7854 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3417 Z= 0.288 Angle : 0.563 10.029 4659 Z= 0.274 Chirality : 0.041 0.131 537 Planarity : 0.003 0.026 566 Dihedral : 7.842 67.498 474 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.42 % Allowed : 12.46 % Favored : 86.12 % Cbeta Deviations : 0.26 % 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: 0.18 (0.40), residues: 409 helix: 0.44 (0.28), residues: 321 sheet: None (None), residues: 0 loop : -0.66 (0.61), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.002 0.001 HIS A 358 PHE 0.028 0.001 PHE A 322 TYR 0.011 0.001 TYR A 149 ARG 0.006 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 161 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7238 (mp) REVERT: A 294 GLU cc_start: 0.8157 (tt0) cc_final: 0.7636 (tt0) outliers start: 5 outliers final: 3 residues processed: 38 average time/residue: 0.8712 time to fit residues: 34.7374 Evaluate side-chains 36 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7825 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3417 Z= 0.195 Angle : 0.524 9.963 4659 Z= 0.253 Chirality : 0.039 0.136 537 Planarity : 0.003 0.026 566 Dihedral : 7.587 65.878 474 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.70 % Allowed : 11.90 % Favored : 86.40 % Cbeta Deviations : 0.26 % 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: 0.54 (0.40), residues: 409 helix: 0.67 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -0.42 (0.61), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.007 0.001 PHE A 372 TYR 0.009 0.001 TYR A 149 ARG 0.005 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.384 Fit side-chains REVERT: A 161 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7190 (mp) REVERT: A 294 GLU cc_start: 0.8157 (tt0) cc_final: 0.7638 (tt0) REVERT: A 456 ARG cc_start: 0.6309 (mmt90) cc_final: 0.6092 (mmp80) outliers start: 6 outliers final: 3 residues processed: 37 average time/residue: 0.8739 time to fit residues: 33.9226 Evaluate side-chains 36 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.0060 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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: 0.7819 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3417 Z= 0.182 Angle : 0.518 9.995 4659 Z= 0.251 Chirality : 0.038 0.143 537 Planarity : 0.003 0.025 566 Dihedral : 7.496 64.888 474 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.42 % Allowed : 12.46 % Favored : 86.12 % Cbeta Deviations : 0.26 % 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 (0.41), residues: 409 helix: 0.81 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -0.41 (0.61), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.026 0.001 PHE A 322 TYR 0.012 0.001 TYR A 155 ARG 0.005 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.373 Fit side-chains REVERT: A 161 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7028 (mm) REVERT: A 294 GLU cc_start: 0.8160 (tt0) cc_final: 0.7635 (tt0) REVERT: A 456 ARG cc_start: 0.6293 (mmt90) cc_final: 0.6085 (mmp80) outliers start: 5 outliers final: 3 residues processed: 37 average time/residue: 0.8781 time to fit residues: 34.1044 Evaluate side-chains 36 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.3980 chunk 9 optimal weight: 0.0060 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.0050 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.3610 ------------------------------------------------------------------------------- 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: 0.7791 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3417 Z= 0.137 Angle : 0.504 10.043 4659 Z= 0.243 Chirality : 0.037 0.148 537 Planarity : 0.003 0.025 566 Dihedral : 7.272 62.689 474 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.85 % Allowed : 13.60 % Favored : 85.55 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.41), residues: 409 helix: 1.03 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -0.34 (0.61), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.001 0.000 HIS A 355 PHE 0.006 0.001 PHE A 211 TYR 0.008 0.001 TYR A 149 ARG 0.005 0.000 ARG A 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.390 Fit side-chains REVERT: A 161 LEU cc_start: 0.7393 (pp) cc_final: 0.7020 (mm) REVERT: A 294 GLU cc_start: 0.8138 (tt0) cc_final: 0.7627 (tt0) REVERT: A 456 ARG cc_start: 0.6199 (mmt90) cc_final: 0.5967 (mmp80) outliers start: 3 outliers final: 2 residues processed: 34 average time/residue: 0.9944 time to fit residues: 35.3571 Evaluate side-chains 33 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 31 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.1980 chunk 36 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 = 0.3070 r_free = 0.3070 target = 0.099807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.080713 restraints weight = 16232.986| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 2.95 r_work: 0.2622 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3417 Z= 0.144 Angle : 0.506 10.020 4659 Z= 0.245 Chirality : 0.038 0.152 537 Planarity : 0.003 0.025 566 Dihedral : 7.216 62.283 474 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.28 % Allowed : 14.16 % Favored : 85.55 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.41), residues: 409 helix: 1.15 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -0.32 (0.61), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.001 0.000 HIS A 355 PHE 0.028 0.001 PHE A 322 TYR 0.013 0.001 TYR A 155 ARG 0.005 0.000 ARG A 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1548.47 seconds wall clock time: 28 minutes 23.06 seconds (1703.06 seconds total)