Starting phenix.real_space_refine on Thu Nov 14 17:36:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8in8_35592/11_2024/8in8_35592.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8in8_35592/11_2024/8in8_35592.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8in8_35592/11_2024/8in8_35592.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8in8_35592/11_2024/8in8_35592.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8in8_35592/11_2024/8in8_35592.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8in8_35592/11_2024/8in8_35592.cif" } 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= 0.001 sd= 0.072 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: 6 Type Number sf(0) Gaussians P 47 5.49 5 Mg 1 5.21 5 S 22 5.16 5 C 4098 2.51 5 N 1140 2.21 5 O 1355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 6663 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2009 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 244} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3685 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 28, 'TRANS': 441} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "I" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 506 Classifications: {'RNA': 24} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 13} Link IDs: {'rna2p': 2, 'rna3p': 21} Chain: "J" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 462 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.83, per 1000 atoms: 0.87 Number of scatterers: 6663 At special positions: 0 Unit cell: (71.6214, 87.0336, 107.885, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 22 16.00 P 47 15.00 Mg 1 11.99 O 1355 8.00 N 1140 7.00 C 4098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 653.2 milliseconds 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1352 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 12 sheets defined 36.0% alpha, 20.7% beta 17 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'B' and resid 356 through 367 Processing helix chain 'B' and resid 383 through 391 removed outlier: 3.604A pdb=" N ILE B 387 " --> pdb=" O GLY B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 414 Processing helix chain 'B' and resid 414 through 430 removed outlier: 3.694A pdb=" N LYS B 418 " --> pdb=" O SER B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 459 through 466 removed outlier: 3.616A pdb=" N ALA B 464 " --> pdb=" O ASP B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 519 removed outlier: 3.688A pdb=" N ARG B 516 " --> pdb=" O PRO B 513 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N GLU B 518 " --> pdb=" O ASP B 515 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU B 519 " --> pdb=" O ARG B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 529 Processing helix chain 'B' and resid 532 through 549 Processing helix chain 'C' and resid 29 through 37 Processing helix chain 'C' and resid 39 through 43 Processing helix chain 'C' and resid 60 through 73 removed outlier: 3.693A pdb=" N LEU C 64 " --> pdb=" O HIS C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 95 Processing helix chain 'C' and resid 111 through 120 removed outlier: 4.191A pdb=" N GLY C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN C 119 " --> pdb=" O GLY C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 134 Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 151 through 157 removed outlier: 4.931A pdb=" N LYS C 156 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 Processing helix chain 'C' and resid 184 through 190 removed outlier: 3.736A pdb=" N LEU C 188 " --> pdb=" O ASN C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 208 removed outlier: 4.008A pdb=" N VAL C 196 " --> pdb=" O CYS C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 295 removed outlier: 3.542A pdb=" N LYS C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 322 Processing helix chain 'C' and resid 418 through 430 removed outlier: 3.872A pdb=" N LYS C 430 " --> pdb=" O LEU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 459 Processing helix chain 'C' and resid 470 through 473 removed outlier: 3.997A pdb=" N MET C 473 " --> pdb=" O ARG C 470 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 470 through 473' Processing sheet with id=AA1, first strand: chain 'B' and resid 579 through 581 removed outlier: 3.812A pdb=" N ALA C 355 " --> pdb=" O ASP C 346 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 335 through 337 removed outlier: 4.098A pdb=" N HIS B 444 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 335 through 337 Processing sheet with id=AA4, first strand: chain 'B' and resid 371 through 373 removed outlier: 3.819A pdb=" N VAL B 378 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 556 through 561 Processing sheet with id=AA6, first strand: chain 'C' and resid 12 through 13 Processing sheet with id=AA7, first strand: chain 'C' and resid 25 through 27 Processing sheet with id=AA8, first strand: chain 'C' and resid 106 through 108 removed outlier: 3.939A pdb=" N CYS C 107 " --> pdb=" O TYR C 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA C 56 " --> pdb=" O CYS C 107 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA C 53 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N TYR C 149 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU C 55 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 159 through 160 removed outlier: 3.550A pdb=" N TYR C 160 " --> pdb=" O PHE C 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 306 through 307 removed outlier: 4.151A pdb=" N TYR C 224 " --> pdb=" O PHE C 248 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR C 467 " --> pdb=" O ALA C 259 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 302 through 303 Processing sheet with id=AB3, first strand: chain 'C' and resid 381 through 382 255 hydrogen bonds defined for protein. 690 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1657 1.33 - 1.45: 1554 1.45 - 1.57: 3578 1.57 - 1.69: 92 1.69 - 1.81: 32 Bond restraints: 6913 Sorted by residual: bond pdb=" C3' DA J 1 " pdb=" O3' DA J 1 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.66e+00 bond pdb=" CB ARG C 138 " pdb=" CG ARG C 138 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.61e+00 bond pdb=" C3' DC J -1 " pdb=" O3' DC J -1 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.25e+00 bond pdb=" CG LEU B 426 " pdb=" CD1 LEU B 426 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.11e+00 bond pdb=" CG PRO C 273 " pdb=" CD PRO C 273 " ideal model delta sigma weight residual 1.503 1.468 0.035 3.40e-02 8.65e+02 1.05e+00 ... (remaining 6908 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 9482 2.52 - 5.04: 92 5.04 - 7.55: 10 7.55 - 10.07: 1 10.07 - 12.59: 1 Bond angle restraints: 9586 Sorted by residual: angle pdb=" CA GLU B 508 " pdb=" CB GLU B 508 " pdb=" CG GLU B 508 " ideal model delta sigma weight residual 114.10 121.58 -7.48 2.00e+00 2.50e-01 1.40e+01 angle pdb=" CA LEU C 98 " pdb=" CB LEU C 98 " pdb=" CG LEU C 98 " ideal model delta sigma weight residual 116.30 128.89 -12.59 3.50e+00 8.16e-02 1.29e+01 angle pdb=" CB MET C 299 " pdb=" CG MET C 299 " pdb=" SD MET C 299 " ideal model delta sigma weight residual 112.70 121.32 -8.62 3.00e+00 1.11e-01 8.25e+00 angle pdb=" CA ARG C 138 " pdb=" CB ARG C 138 " pdb=" CG ARG C 138 " ideal model delta sigma weight residual 114.10 119.46 -5.36 2.00e+00 2.50e-01 7.17e+00 angle pdb=" CA PRO C 273 " pdb=" N PRO C 273 " pdb=" CD PRO C 273 " ideal model delta sigma weight residual 112.00 108.37 3.63 1.40e+00 5.10e-01 6.73e+00 ... (remaining 9581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.12: 3813 35.12 - 70.25: 289 70.25 - 105.37: 15 105.37 - 140.50: 1 140.50 - 175.62: 3 Dihedral angle restraints: 4121 sinusoidal: 2018 harmonic: 2103 Sorted by residual: dihedral pdb=" CA PHE B 328 " pdb=" C PHE B 328 " pdb=" N PRO B 329 " pdb=" CA PRO B 329 " ideal model delta harmonic sigma weight residual 180.00 153.35 26.65 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA VAL C 463 " pdb=" C VAL C 463 " pdb=" N ASN C 464 " pdb=" CA ASN C 464 " ideal model delta harmonic sigma weight residual -180.00 -155.78 -24.22 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA ILE C 14 " pdb=" C ILE C 14 " pdb=" N PRO C 15 " pdb=" CA PRO C 15 " ideal model delta harmonic sigma weight residual 180.00 -157.56 -22.44 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 4118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 684 0.029 - 0.059: 269 0.059 - 0.088: 71 0.088 - 0.117: 45 0.117 - 0.147: 17 Chirality restraints: 1086 Sorted by residual: chirality pdb=" C1' G I 7 " pdb=" O4' G I 7 " pdb=" C2' G I 7 " pdb=" N9 G I 7 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA ILE C 407 " pdb=" N ILE C 407 " pdb=" C ILE C 407 " pdb=" CB ILE C 407 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CB ILE C 305 " pdb=" CA ILE C 305 " pdb=" CG1 ILE C 305 " pdb=" CG2 ILE C 305 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 1083 not shown) Planarity restraints: 1063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 272 " 0.058 5.00e-02 4.00e+02 8.58e-02 1.18e+01 pdb=" N PRO C 273 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 273 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 273 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 56 " 0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO C 57 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 57 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 57 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U I 5 " 0.025 2.00e-02 2.50e+03 1.25e-02 3.53e+00 pdb=" N1 U I 5 " -0.026 2.00e-02 2.50e+03 pdb=" C2 U I 5 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U I 5 " -0.004 2.00e-02 2.50e+03 pdb=" N3 U I 5 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U I 5 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U I 5 " 0.007 2.00e-02 2.50e+03 pdb=" C5 U I 5 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U I 5 " -0.005 2.00e-02 2.50e+03 ... (remaining 1060 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 43 2.54 - 3.13: 4720 3.13 - 3.72: 10334 3.72 - 4.31: 14501 4.31 - 4.90: 23667 Nonbonded interactions: 53265 Sorted by model distance: nonbonded pdb=" OP1 A I 1 " pdb="MG MG I 101 " model vdw 1.950 2.170 nonbonded pdb=" OP3 A I 1 " pdb="MG MG I 101 " model vdw 2.001 2.170 nonbonded pdb=" O MET C 473 " pdb="MG MG I 101 " model vdw 2.015 2.170 nonbonded pdb=" O GLN C 281 " pdb=" OG SER C 285 " model vdw 2.225 3.040 nonbonded pdb=" O LEU C 426 " pdb=" OG1 THR C 429 " model vdw 2.233 3.040 ... (remaining 53260 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.080 Process input model: 22.510 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 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 : 0.003 0.046 6913 Z= 0.187 Angle : 0.615 12.588 9586 Z= 0.325 Chirality : 0.040 0.147 1086 Planarity : 0.005 0.086 1063 Dihedral : 21.500 175.621 2769 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.13 % Favored : 93.73 % Rotamer: Outliers : 3.63 % Allowed : 33.50 % Favored : 62.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.32), residues: 718 helix: 1.49 (0.37), residues: 211 sheet: -0.16 (0.44), residues: 160 loop : -1.30 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 502 HIS 0.003 0.001 HIS B 437 PHE 0.010 0.001 PHE C 158 TYR 0.013 0.001 TYR C 469 ARG 0.008 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.674 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 21 residues processed: 75 average time/residue: 0.9181 time to fit residues: 73.9841 Evaluate side-chains 74 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 447 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 23 optimal weight: 0.0060 chunk 36 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.0721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6913 Z= 0.165 Angle : 0.557 8.582 9586 Z= 0.295 Chirality : 0.039 0.136 1086 Planarity : 0.005 0.058 1063 Dihedral : 19.474 173.851 1455 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.29 % Allowed : 30.53 % Favored : 65.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.32), residues: 718 helix: 1.66 (0.36), residues: 224 sheet: 0.12 (0.44), residues: 156 loop : -1.29 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 502 HIS 0.003 0.001 HIS C 306 PHE 0.007 0.001 PHE C 158 TYR 0.009 0.001 TYR C 341 ARG 0.005 0.000 ARG C 263 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.635 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 83 average time/residue: 0.9251 time to fit residues: 82.5915 Evaluate side-chains 71 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 407 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 57 optimal weight: 0.3980 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 558 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6913 Z= 0.212 Angle : 0.584 8.327 9586 Z= 0.309 Chirality : 0.042 0.201 1086 Planarity : 0.005 0.056 1063 Dihedral : 19.463 174.865 1438 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 4.62 % Allowed : 31.85 % Favored : 63.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.12 (0.32), residues: 718 helix: 1.58 (0.36), residues: 224 sheet: 0.11 (0.43), residues: 157 loop : -1.35 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 377 HIS 0.003 0.001 HIS C 166 PHE 0.009 0.001 PHE C 158 TYR 0.015 0.001 TYR C 341 ARG 0.006 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 58 time to evaluate : 1.260 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 9 residues processed: 80 average time/residue: 0.9890 time to fit residues: 85.3080 Evaluate side-chains 66 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 407 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 7 optimal weight: 0.0070 chunk 32 optimal weight: 0.0000 chunk 46 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 0.0770 chunk 19 optimal weight: 2.9990 overall best weight: 0.6164 ------------------------------------------------------------------------------- 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: 0.7351 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6913 Z= 0.168 Angle : 0.550 7.240 9586 Z= 0.292 Chirality : 0.040 0.180 1086 Planarity : 0.005 0.053 1063 Dihedral : 19.395 174.982 1437 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.63 % Allowed : 33.33 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.06 (0.32), residues: 718 helix: 1.77 (0.35), residues: 226 sheet: 0.25 (0.44), residues: 154 loop : -1.30 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 502 HIS 0.003 0.001 HIS C 306 PHE 0.006 0.001 PHE C 158 TYR 0.010 0.001 TYR C 341 ARG 0.006 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: C 260 TYR cc_start: 0.7729 (OUTLIER) cc_final: 0.7099 (p90) outliers start: 22 outliers final: 7 residues processed: 78 average time/residue: 0.9031 time to fit residues: 75.6830 Evaluate side-chains 63 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 407 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 54 optimal weight: 0.0870 chunk 30 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 65 optimal weight: 0.4980 chunk 18 optimal weight: 4.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 477 ASN B 558 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6913 Z= 0.165 Angle : 0.542 6.812 9586 Z= 0.289 Chirality : 0.040 0.185 1086 Planarity : 0.005 0.056 1063 Dihedral : 19.358 175.610 1437 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.46 % Allowed : 32.84 % Favored : 62.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.17 (0.33), residues: 718 helix: 1.84 (0.35), residues: 226 sheet: 0.35 (0.44), residues: 156 loop : -1.25 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 502 HIS 0.003 0.001 HIS C 306 PHE 0.007 0.001 PHE C 158 TYR 0.009 0.001 TYR C 341 ARG 0.006 0.000 ARG C 263 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: C 119 ASN cc_start: 0.7450 (p0) cc_final: 0.6794 (m110) REVERT: C 346 ASP cc_start: 0.7625 (m-30) cc_final: 0.7012 (m-30) outliers start: 27 outliers final: 10 residues processed: 82 average time/residue: 0.9021 time to fit residues: 79.4243 Evaluate side-chains 67 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 407 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.0010 chunk 66 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 61 optimal weight: 0.0770 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 overall best weight: 3.0150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 558 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 6913 Z= 0.440 Angle : 0.733 6.420 9586 Z= 0.388 Chirality : 0.050 0.272 1086 Planarity : 0.006 0.066 1063 Dihedral : 19.688 175.278 1435 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.69 % Favored : 93.18 % Rotamer: Outliers : 4.62 % Allowed : 32.84 % Favored : 62.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -0.69 (0.31), residues: 718 helix: 0.83 (0.35), residues: 223 sheet: 0.07 (0.43), residues: 157 loop : -1.63 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP C 377 HIS 0.005 0.002 HIS B 444 PHE 0.017 0.002 PHE C 143 TYR 0.035 0.003 TYR C 341 ARG 0.010 0.001 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 63 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: C 352 LYS cc_start: 0.6830 (OUTLIER) cc_final: 0.5856 (tttt) outliers start: 28 outliers final: 15 residues processed: 86 average time/residue: 1.0451 time to fit residues: 95.8380 Evaluate side-chains 76 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 462 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 45 optimal weight: 0.0670 chunk 44 optimal weight: 0.8980 chunk 33 optimal weight: 0.0000 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.5122 ------------------------------------------------------------------------------- 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: 0.7379 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6913 Z= 0.178 Angle : 0.595 8.672 9586 Z= 0.316 Chirality : 0.041 0.165 1086 Planarity : 0.005 0.061 1063 Dihedral : 19.522 174.997 1435 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.64 % Allowed : 34.32 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -0.10 (0.32), residues: 718 helix: 1.59 (0.36), residues: 214 sheet: 0.08 (0.44), residues: 158 loop : -1.23 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 502 HIS 0.003 0.001 HIS C 306 PHE 0.007 0.001 PHE C 90 TYR 0.010 0.001 TYR C 359 ARG 0.007 0.001 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: C 119 ASN cc_start: 0.7484 (p0) cc_final: 0.6857 (m110) REVERT: C 346 ASP cc_start: 0.7655 (m-30) cc_final: 0.7086 (m-30) outliers start: 16 outliers final: 8 residues processed: 76 average time/residue: 1.0020 time to fit residues: 81.6124 Evaluate side-chains 68 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 407 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 0.2980 chunk 64 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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: 0.7444 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6913 Z= 0.249 Angle : 0.632 8.065 9586 Z= 0.333 Chirality : 0.043 0.184 1086 Planarity : 0.005 0.066 1063 Dihedral : 19.560 175.787 1435 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.41 % Favored : 93.45 % Rotamer: Outliers : 2.48 % Allowed : 34.98 % Favored : 62.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -0.29 (0.32), residues: 718 helix: 1.40 (0.36), residues: 217 sheet: 0.06 (0.44), residues: 157 loop : -1.38 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 502 HIS 0.002 0.001 HIS C 306 PHE 0.009 0.001 PHE C 471 TYR 0.019 0.002 TYR C 341 ARG 0.008 0.001 ARG C 263 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: C 119 ASN cc_start: 0.7447 (p0) cc_final: 0.6761 (m110) REVERT: C 346 ASP cc_start: 0.7736 (m-30) cc_final: 0.7140 (m-30) REVERT: C 352 LYS cc_start: 0.6721 (OUTLIER) cc_final: 0.5970 (tttt) outliers start: 15 outliers final: 9 residues processed: 74 average time/residue: 1.0939 time to fit residues: 86.2409 Evaluate side-chains 71 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 462 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 64 optimal weight: 0.0980 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6913 Z= 0.195 Angle : 0.610 8.901 9586 Z= 0.320 Chirality : 0.041 0.166 1086 Planarity : 0.005 0.065 1063 Dihedral : 19.514 176.208 1435 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.48 % Allowed : 35.48 % Favored : 62.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -0.11 (0.32), residues: 718 helix: 1.51 (0.35), residues: 220 sheet: 0.15 (0.44), residues: 158 loop : -1.27 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 502 HIS 0.003 0.001 HIS C 306 PHE 0.008 0.001 PHE C 158 TYR 0.013 0.001 TYR C 341 ARG 0.007 0.001 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: C 119 ASN cc_start: 0.7512 (p0) cc_final: 0.6912 (m-40) REVERT: C 346 ASP cc_start: 0.7645 (m-30) cc_final: 0.7091 (m-30) REVERT: C 352 LYS cc_start: 0.6737 (OUTLIER) cc_final: 0.5999 (tttt) outliers start: 15 outliers final: 10 residues processed: 75 average time/residue: 1.2369 time to fit residues: 98.7301 Evaluate side-chains 74 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 462 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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: 0.7486 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6913 Z= 0.326 Angle : 0.697 8.885 9586 Z= 0.365 Chirality : 0.046 0.243 1086 Planarity : 0.006 0.069 1063 Dihedral : 19.693 176.135 1435 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.82 % Favored : 93.04 % Rotamer: Outliers : 2.15 % Allowed : 36.14 % Favored : 61.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.31), residues: 718 helix: 1.13 (0.35), residues: 217 sheet: 0.18 (0.44), residues: 149 loop : -1.49 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 502 HIS 0.003 0.001 HIS C 166 PHE 0.012 0.002 PHE C 143 TYR 0.026 0.002 TYR C 341 ARG 0.008 0.001 ARG C 263 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: C 346 ASP cc_start: 0.7759 (m-30) cc_final: 0.7152 (m-30) REVERT: C 352 LYS cc_start: 0.6772 (OUTLIER) cc_final: 0.6004 (tttt) outliers start: 13 outliers final: 9 residues processed: 72 average time/residue: 1.2428 time to fit residues: 95.1955 Evaluate side-chains 71 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 407 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4103 r_free = 0.4103 target = 0.158813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.126938 restraints weight = 7852.373| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 1.96 r_work: 0.3596 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6913 Z= 0.223 Angle : 0.644 10.376 9586 Z= 0.338 Chirality : 0.043 0.165 1086 Planarity : 0.005 0.067 1063 Dihedral : 19.640 176.148 1435 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.98 % Allowed : 36.30 % Favored : 61.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -0.29 (0.32), residues: 718 helix: 1.43 (0.36), residues: 212 sheet: 0.02 (0.43), residues: 158 loop : -1.34 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 502 HIS 0.003 0.001 HIS C 306 PHE 0.008 0.001 PHE C 90 TYR 0.016 0.002 TYR C 341 ARG 0.007 0.001 ARG C 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2386.16 seconds wall clock time: 44 minutes 6.72 seconds (2646.72 seconds total)