Starting phenix.real_space_refine on Sun Mar 10 20:37:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9p_31035/03_2024/7e9p_31035.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9p_31035/03_2024/7e9p_31035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9p_31035/03_2024/7e9p_31035.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9p_31035/03_2024/7e9p_31035.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9p_31035/03_2024/7e9p_31035.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9p_31035/03_2024/7e9p_31035.pdb" } resolution = 3.69 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= -0.004 sd= 0.036 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 22 5.16 5 C 3095 2.51 5 N 823 2.21 5 O 958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 398": "OD1" <-> "OD2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "L ASP 1": "OD1" <-> "OD2" Residue "L TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 39": "OD1" <-> "OD2" Residue "L TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 86": "OE1" <-> "OE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 148": "OE1" <-> "OE2" Residue "L GLU 170": "OE1" <-> "OE2" Residue "L GLU 200": "OE1" <-> "OE2" Residue "H ARG 19": "NH1" <-> "NH2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H ASP 62": "OD1" <-> "OD2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 4898 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "L" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "H" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1668 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.26, per 1000 atoms: 0.67 Number of scatterers: 4898 At special positions: 0 Unit cell: (70.08, 102.93, 98.55, 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 22 16.00 O 958 8.00 N 823 7.00 C 3095 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.04 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 157 " - pdb=" SG CYS H 213 " distance=2.04 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 Links applied NAG-ASN " NAG B1301 " - " ASN B 343 " Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 938.2 milliseconds 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1170 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 11 sheets defined 8.3% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.512A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.520A pdb=" N ALA B 352 " --> pdb=" O SER B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.529A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 5.674A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.761A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'L' and resid 126 through 130 Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.114A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 175 No H-bonds generated for 'chain 'H' and resid 173 through 175' Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.603A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.562A pdb=" N LEU L 11 " --> pdb=" O LYS L 108 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP L 110 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 119 through 123 removed outlier: 5.920A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 158 through 159 removed outlier: 3.771A pdb=" N VAL L 155 " --> pdb=" O ALA L 158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.666A pdb=" N THR H 124 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR H 94 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL H 126 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 137 through 141 removed outlier: 6.009A pdb=" N TYR H 193 " --> pdb=" O ASP H 161 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 167 through 171 162 hydrogen bonds defined for protein. 387 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: 1.28 Time building geometry restraints manager: 1.96 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: 802 1.31 - 1.44: 1423 1.44 - 1.57: 2765 1.57 - 1.70: 0 1.70 - 1.83: 28 Bond restraints: 5018 Sorted by residual: bond pdb=" C7 NAG B1301 " pdb=" N2 NAG B1301 " ideal model delta sigma weight residual 1.346 1.454 -0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.502 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" N GLU B 484 " pdb=" CA GLU B 484 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.27e-02 6.20e+03 1.33e+01 bond pdb=" N LEU H 206 " pdb=" CA LEU H 206 " ideal model delta sigma weight residual 1.458 1.503 -0.045 1.27e-02 6.20e+03 1.26e+01 bond pdb=" N VAL B 483 " pdb=" CA VAL B 483 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.17e+01 ... (remaining 5013 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.51: 170 106.51 - 113.37: 2664 113.37 - 120.23: 1715 120.23 - 127.09: 2222 127.09 - 133.95: 58 Bond angle restraints: 6829 Sorted by residual: angle pdb=" N PHE B 486 " pdb=" CA PHE B 486 " pdb=" C PHE B 486 " ideal model delta sigma weight residual 112.97 105.34 7.63 1.06e+00 8.90e-01 5.18e+01 angle pdb=" CA VAL B 483 " pdb=" C VAL B 483 " pdb=" O VAL B 483 " ideal model delta sigma weight residual 121.63 114.88 6.75 9.90e-01 1.02e+00 4.66e+01 angle pdb=" C GLU B 484 " pdb=" CA GLU B 484 " pdb=" CB GLU B 484 " ideal model delta sigma weight residual 110.78 101.60 9.18 1.60e+00 3.91e-01 3.29e+01 angle pdb=" N GLU B 484 " pdb=" CA GLU B 484 " pdb=" C GLU B 484 " ideal model delta sigma weight residual 108.20 117.66 -9.46 1.71e+00 3.42e-01 3.06e+01 angle pdb=" CB GLN B 474 " pdb=" CG GLN B 474 " pdb=" CD GLN B 474 " ideal model delta sigma weight residual 112.60 105.42 7.18 1.70e+00 3.46e-01 1.78e+01 ... (remaining 6824 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.00: 2774 23.00 - 46.00: 184 46.00 - 69.00: 23 69.00 - 92.00: 3 92.00 - 115.00: 8 Dihedral angle restraints: 2992 sinusoidal: 1154 harmonic: 1838 Sorted by residual: dihedral pdb=" CB CYS H 157 " pdb=" SG CYS H 157 " pdb=" SG CYS H 213 " pdb=" CB CYS H 213 " ideal model delta sinusoidal sigma weight residual 93.00 141.21 -48.21 1 1.00e+01 1.00e-02 3.20e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 48.54 44.46 1 1.00e+01 1.00e-02 2.75e+01 dihedral pdb=" CA CYS B 361 " pdb=" C CYS B 361 " pdb=" N VAL B 362 " pdb=" CA VAL B 362 " ideal model delta harmonic sigma weight residual 180.00 157.14 22.86 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 2989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 583 0.052 - 0.105: 144 0.105 - 0.157: 23 0.157 - 0.210: 4 0.210 - 0.262: 1 Chirality restraints: 755 Sorted by residual: chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA LEU H 206 " pdb=" N LEU H 206 " pdb=" C LEU H 206 " pdb=" CB LEU H 206 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" CA PHE B 486 " pdb=" N PHE B 486 " pdb=" C PHE B 486 " pdb=" CB PHE B 486 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.76e-01 ... (remaining 752 not shown) Planarity restraints: 886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 473 " 0.014 2.00e-02 2.50e+03 1.41e-02 3.96e+00 pdb=" CG TYR B 473 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR B 473 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR B 473 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 473 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 473 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 473 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 473 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 453 " 0.015 2.00e-02 2.50e+03 1.15e-02 2.65e+00 pdb=" CG TYR B 453 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 453 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 453 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 453 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 453 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 453 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 453 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 473 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.60e+00 pdb=" C TYR B 473 " 0.028 2.00e-02 2.50e+03 pdb=" O TYR B 473 " -0.011 2.00e-02 2.50e+03 pdb=" N GLN B 474 " -0.009 2.00e-02 2.50e+03 ... (remaining 883 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 690 2.75 - 3.29: 4535 3.29 - 3.83: 7332 3.83 - 4.36: 8186 4.36 - 4.90: 15089 Nonbonded interactions: 35832 Sorted by model distance: nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.218 2.440 nonbonded pdb=" OG SER B 349 " pdb=" O LEU B 452 " model vdw 2.221 2.440 nonbonded pdb=" O SER H 52 " pdb=" NH1 ARG H 72 " model vdw 2.260 2.520 nonbonded pdb=" OG SER B 443 " pdb=" O PHE B 497 " model vdw 2.278 2.440 nonbonded pdb=" O ARG L 147 " pdb=" NH1 ARG L 147 " model vdw 2.304 2.520 ... (remaining 35827 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.560 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 17.630 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 : 0.005 0.108 5018 Z= 0.347 Angle : 0.783 9.461 6829 Z= 0.456 Chirality : 0.048 0.262 755 Planarity : 0.004 0.038 885 Dihedral : 16.126 115.002 1801 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % 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: -2.51 (0.31), residues: 629 helix: -3.97 (0.66), residues: 25 sheet: -0.64 (0.33), residues: 240 loop : -2.30 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 436 HIS 0.006 0.001 HIS H 35 PHE 0.020 0.001 PHE H 139 TYR 0.034 0.002 TYR B 473 ARG 0.005 0.001 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 434 ILE cc_start: 0.8922 (mp) cc_final: 0.8705 (mt) REVERT: H 30 ASP cc_start: 0.7983 (p0) cc_final: 0.7570 (p0) REVERT: H 31 ASP cc_start: 0.8192 (m-30) cc_final: 0.7574 (m-30) REVERT: H 161 ASP cc_start: 0.8187 (m-30) cc_final: 0.7939 (m-30) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1649 time to fit residues: 15.0515 Evaluate side-chains 61 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 0.0050 chunk 56 optimal weight: 0.6980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 ASN H 221 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5018 Z= 0.190 Angle : 0.624 9.258 6829 Z= 0.312 Chirality : 0.045 0.253 755 Planarity : 0.004 0.037 885 Dihedral : 7.732 58.040 713 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.55 % Allowed : 9.24 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % 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: -2.28 (0.32), residues: 629 helix: -4.05 (0.66), residues: 25 sheet: -0.50 (0.33), residues: 241 loop : -2.11 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.005 0.001 HIS H 35 PHE 0.012 0.001 PHE H 139 TYR 0.017 0.001 TYR B 453 ARG 0.002 0.000 ARG L 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 434 ILE cc_start: 0.8961 (mp) cc_final: 0.8754 (mt) REVERT: H 30 ASP cc_start: 0.8204 (p0) cc_final: 0.7919 (p0) REVERT: H 31 ASP cc_start: 0.8143 (m-30) cc_final: 0.7619 (m-30) REVERT: H 161 ASP cc_start: 0.8233 (m-30) cc_final: 0.8005 (m-30) REVERT: H 221 ASN cc_start: 0.7383 (OUTLIER) cc_final: 0.7166 (p0) outliers start: 3 outliers final: 1 residues processed: 65 average time/residue: 0.1522 time to fit residues: 13.3395 Evaluate side-chains 54 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain H residue 221 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 15 optimal weight: 0.4980 chunk 56 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 221 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5018 Z= 0.205 Angle : 0.601 6.393 6829 Z= 0.303 Chirality : 0.045 0.289 755 Planarity : 0.004 0.035 885 Dihedral : 5.276 30.996 713 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.11 % Allowed : 13.86 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % 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: -2.03 (0.32), residues: 629 helix: -3.39 (0.77), residues: 25 sheet: -0.18 (0.34), residues: 232 loop : -2.07 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.005 0.001 HIS H 35 PHE 0.011 0.001 PHE B 456 TYR 0.029 0.001 TYR B 473 ARG 0.002 0.000 ARG L 147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: B 434 ILE cc_start: 0.8968 (mp) cc_final: 0.8768 (mt) REVERT: H 30 ASP cc_start: 0.8288 (p0) cc_final: 0.7961 (p0) REVERT: H 31 ASP cc_start: 0.8130 (m-30) cc_final: 0.7586 (m-30) REVERT: H 161 ASP cc_start: 0.8180 (m-30) cc_final: 0.7953 (m-30) REVERT: H 221 ASN cc_start: 0.7352 (OUTLIER) cc_final: 0.7143 (p0) outliers start: 6 outliers final: 3 residues processed: 65 average time/residue: 0.1713 time to fit residues: 14.6661 Evaluate side-chains 59 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain H residue 221 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 129 GLN H 221 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5018 Z= 0.270 Angle : 0.665 10.088 6829 Z= 0.336 Chirality : 0.047 0.280 755 Planarity : 0.004 0.036 885 Dihedral : 5.064 29.822 713 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.22 % Allowed : 15.34 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % 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: -2.09 (0.32), residues: 629 helix: -3.60 (0.77), residues: 18 sheet: -0.32 (0.34), residues: 242 loop : -2.11 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 436 HIS 0.004 0.001 HIS H 35 PHE 0.011 0.001 PHE L 144 TYR 0.031 0.002 TYR B 473 ARG 0.006 0.001 ARG L 216 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: B 434 ILE cc_start: 0.8986 (mp) cc_final: 0.8786 (mt) REVERT: L 150 LYS cc_start: 0.7795 (tmtt) cc_final: 0.7260 (tptp) REVERT: H 30 ASP cc_start: 0.8194 (p0) cc_final: 0.7933 (p0) REVERT: H 31 ASP cc_start: 0.8184 (m-30) cc_final: 0.7631 (m-30) REVERT: H 161 ASP cc_start: 0.8071 (m-30) cc_final: 0.7850 (m-30) outliers start: 12 outliers final: 7 residues processed: 68 average time/residue: 0.1687 time to fit residues: 15.0609 Evaluate side-chains 61 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 159 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 41 optimal weight: 0.4980 chunk 30 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.7955 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5018 Z= 0.202 Angle : 0.638 12.286 6829 Z= 0.319 Chirality : 0.045 0.244 755 Planarity : 0.004 0.034 885 Dihedral : 4.748 26.491 713 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.03 % Allowed : 16.64 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % 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: -1.96 (0.32), residues: 629 helix: -3.27 (1.06), residues: 12 sheet: -0.20 (0.34), residues: 242 loop : -2.08 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 436 HIS 0.005 0.001 HIS H 35 PHE 0.014 0.001 PHE B 486 TYR 0.022 0.001 TYR B 473 ARG 0.005 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: B 434 ILE cc_start: 0.8981 (mp) cc_final: 0.8777 (mt) REVERT: L 150 LYS cc_start: 0.7913 (tmtt) cc_final: 0.7406 (tptt) REVERT: H 30 ASP cc_start: 0.8271 (p0) cc_final: 0.7938 (p0) REVERT: H 31 ASP cc_start: 0.8149 (m-30) cc_final: 0.7656 (m-30) REVERT: H 161 ASP cc_start: 0.8127 (m-30) cc_final: 0.7914 (m-30) outliers start: 11 outliers final: 6 residues processed: 66 average time/residue: 0.1749 time to fit residues: 15.1468 Evaluate side-chains 62 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 215 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 57 optimal weight: 0.0030 chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.2594 ------------------------------------------------------------------------------- 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: 0.7991 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5018 Z= 0.264 Angle : 0.667 10.907 6829 Z= 0.335 Chirality : 0.046 0.276 755 Planarity : 0.004 0.037 885 Dihedral : 5.024 29.526 713 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 1.66 % Allowed : 19.04 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % 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: -1.97 (0.32), residues: 629 helix: -3.35 (1.04), residues: 12 sheet: -0.18 (0.34), residues: 242 loop : -2.11 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 436 HIS 0.004 0.001 HIS H 35 PHE 0.015 0.002 PHE B 456 TYR 0.019 0.002 TYR B 453 ARG 0.003 0.000 ARG L 216 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: B 434 ILE cc_start: 0.8997 (mp) cc_final: 0.8792 (mt) REVERT: L 150 LYS cc_start: 0.7886 (tmtt) cc_final: 0.7357 (tptt) REVERT: H 30 ASP cc_start: 0.8229 (p0) cc_final: 0.7900 (p0) REVERT: H 31 ASP cc_start: 0.8189 (m-30) cc_final: 0.7684 (m-30) REVERT: H 161 ASP cc_start: 0.8092 (m-30) cc_final: 0.7876 (m-30) outliers start: 9 outliers final: 8 residues processed: 62 average time/residue: 0.1720 time to fit residues: 14.2303 Evaluate side-chains 62 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 215 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 59 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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: 0.8049 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 5018 Z= 0.402 Angle : 0.766 13.769 6829 Z= 0.385 Chirality : 0.049 0.342 755 Planarity : 0.005 0.042 885 Dihedral : 5.715 33.762 713 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 2.59 % Allowed : 18.67 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % 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: -2.21 (0.32), residues: 629 helix: -4.53 (0.47), residues: 25 sheet: -0.25 (0.33), residues: 242 loop : -2.20 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 436 HIS 0.004 0.001 HIS H 35 PHE 0.020 0.002 PHE L 144 TYR 0.026 0.002 TYR B 453 ARG 0.003 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 52 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: B 470 THR cc_start: 0.8844 (p) cc_final: 0.8594 (p) REVERT: L 86 GLU cc_start: 0.8118 (tp30) cc_final: 0.7869 (tp30) REVERT: L 150 LYS cc_start: 0.8011 (tmtt) cc_final: 0.7441 (tptt) REVERT: H 30 ASP cc_start: 0.8231 (p0) cc_final: 0.7987 (p0) REVERT: H 31 ASP cc_start: 0.8288 (m-30) cc_final: 0.7848 (m-30) REVERT: H 161 ASP cc_start: 0.8160 (m-30) cc_final: 0.7953 (m-30) outliers start: 14 outliers final: 10 residues processed: 63 average time/residue: 0.1781 time to fit residues: 14.7061 Evaluate side-chains 62 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 52 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 215 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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: 0.7980 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5018 Z= 0.216 Angle : 0.639 12.006 6829 Z= 0.319 Chirality : 0.045 0.269 755 Planarity : 0.004 0.038 885 Dihedral : 4.970 28.848 713 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.66 % Allowed : 19.22 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % 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: -1.94 (0.32), residues: 629 helix: -4.13 (0.79), residues: 12 sheet: -0.08 (0.34), residues: 243 loop : -2.13 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 436 HIS 0.005 0.001 HIS H 35 PHE 0.017 0.001 PHE B 456 TYR 0.017 0.001 TYR B 473 ARG 0.002 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: B 470 THR cc_start: 0.8763 (p) cc_final: 0.8513 (p) REVERT: L 150 LYS cc_start: 0.7855 (tmtt) cc_final: 0.7318 (tptt) REVERT: H 30 ASP cc_start: 0.8208 (p0) cc_final: 0.7875 (p0) REVERT: H 31 ASP cc_start: 0.8188 (m-30) cc_final: 0.7677 (m-30) outliers start: 9 outliers final: 7 residues processed: 65 average time/residue: 0.1605 time to fit residues: 13.8487 Evaluate side-chains 60 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 215 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7966 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5018 Z= 0.195 Angle : 0.638 10.622 6829 Z= 0.316 Chirality : 0.044 0.257 755 Planarity : 0.004 0.039 885 Dihedral : 4.778 27.707 713 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.66 % Allowed : 20.52 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % 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: -1.81 (0.32), residues: 629 helix: -4.04 (0.90), residues: 12 sheet: 0.02 (0.34), residues: 242 loop : -2.05 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 436 HIS 0.006 0.001 HIS H 35 PHE 0.024 0.001 PHE B 456 TYR 0.015 0.001 TYR B 473 ARG 0.003 0.000 ARG L 147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: B 470 THR cc_start: 0.8716 (p) cc_final: 0.8483 (p) REVERT: L 86 GLU cc_start: 0.7828 (tp30) cc_final: 0.7602 (tp30) REVERT: L 150 LYS cc_start: 0.7834 (tmtt) cc_final: 0.7285 (tptt) REVERT: H 30 ASP cc_start: 0.8223 (p0) cc_final: 0.7928 (p0) REVERT: H 31 ASP cc_start: 0.8160 (m-30) cc_final: 0.7677 (m-30) REVERT: H 161 ASP cc_start: 0.7831 (m-30) cc_final: 0.7558 (m-30) outliers start: 9 outliers final: 9 residues processed: 60 average time/residue: 0.1795 time to fit residues: 14.2633 Evaluate side-chains 61 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 215 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.1980 chunk 56 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5018 Z= 0.274 Angle : 0.679 11.234 6829 Z= 0.338 Chirality : 0.046 0.288 755 Planarity : 0.004 0.043 885 Dihedral : 5.064 30.057 713 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.85 % Allowed : 20.89 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % 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: -1.83 (0.32), residues: 629 helix: -5.08 (0.28), residues: 6 sheet: 0.03 (0.34), residues: 242 loop : -2.11 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.006 0.001 HIS H 35 PHE 0.014 0.001 PHE B 486 TYR 0.018 0.002 TYR B 453 ARG 0.002 0.000 ARG L 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: B 470 THR cc_start: 0.8763 (p) cc_final: 0.8515 (p) REVERT: L 86 GLU cc_start: 0.7993 (tp30) cc_final: 0.7767 (tp30) REVERT: L 150 LYS cc_start: 0.7876 (tmtt) cc_final: 0.7346 (tptt) REVERT: H 30 ASP cc_start: 0.8228 (p0) cc_final: 0.7931 (p0) REVERT: H 31 ASP cc_start: 0.8193 (m-30) cc_final: 0.7720 (m-30) REVERT: H 161 ASP cc_start: 0.7888 (m-30) cc_final: 0.7611 (m-30) outliers start: 10 outliers final: 9 residues processed: 61 average time/residue: 0.1569 time to fit residues: 12.9706 Evaluate side-chains 62 residues out of total 545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 215 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.102185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.087920 restraints weight = 11393.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.090155 restraints weight = 5692.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.091590 restraints weight = 3431.799| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5018 Z= 0.239 Angle : 0.655 10.572 6829 Z= 0.326 Chirality : 0.045 0.275 755 Planarity : 0.004 0.039 885 Dihedral : 4.947 29.237 713 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.66 % Allowed : 21.07 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.51 % 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: -1.78 (0.32), residues: 629 helix: -5.11 (0.27), residues: 6 sheet: 0.05 (0.34), residues: 242 loop : -2.06 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 436 HIS 0.006 0.001 HIS H 35 PHE 0.014 0.001 PHE B 486 TYR 0.016 0.001 TYR B 453 ARG 0.002 0.000 ARG L 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1290.51 seconds wall clock time: 24 minutes 6.35 seconds (1446.35 seconds total)