Starting phenix.real_space_refine on Sun Mar 10 23:22:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtn_24684/03_2024/7rtn_24684.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtn_24684/03_2024/7rtn_24684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtn_24684/03_2024/7rtn_24684.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtn_24684/03_2024/7rtn_24684.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtn_24684/03_2024/7rtn_24684.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtn_24684/03_2024/7rtn_24684.pdb" } resolution = 3.4 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= 0.002 sd= 0.008 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 12 5.16 5 C 3792 2.51 5 N 1098 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 375": "OD1" <-> "OD2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 400": "OD1" <-> "OD2" Residue "A TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 483": "OD1" <-> "OD2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C PHE 441": "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: 6018 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2006 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 10, 'TRANS': 259} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "B" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2006 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 10, 'TRANS': 259} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "C" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2006 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 10, 'TRANS': 259} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Time building chain proxies: 3.97, per 1000 atoms: 0.66 Number of scatterers: 6018 At special positions: 0 Unit cell: (104.72, 104.72, 111.52, 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 12 16.00 O 1116 8.00 N 1098 7.00 C 3792 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.3 seconds 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1512 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 6 sheets defined 56.7% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 64 through 80 removed outlier: 3.967A pdb=" N SER A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 135 removed outlier: 3.719A pdb=" N ARG A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 340 Proline residue: A 326 - end of helix Processing helix chain 'A' and resid 346 through 353 removed outlier: 3.982A pdb=" N VAL A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET A 352 " --> pdb=" O PRO A 348 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 438 Processing helix chain 'A' and resid 446 through 455 removed outlier: 3.911A pdb=" N ARG A 452 " --> pdb=" O ARG A 448 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR A 455 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 483 Processing helix chain 'A' and resid 484 through 491 Processing helix chain 'A' and resid 494 through 508 Processing helix chain 'B' and resid 65 through 79 removed outlier: 4.009A pdb=" N LYS B 70 " --> pdb=" O GLY B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 135 removed outlier: 3.531A pdb=" N ARG B 93 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN B 135 " --> pdb=" O TYR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 340 removed outlier: 3.970A pdb=" N GLY B 340 " --> pdb=" O LYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.755A pdb=" N PHE B 354 " --> pdb=" O MET B 351 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS B 355 " --> pdb=" O MET B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 438 removed outlier: 3.550A pdb=" N SER B 438 " --> pdb=" O ASN B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 455 removed outlier: 3.953A pdb=" N THR B 455 " --> pdb=" O VAL B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 483 Processing helix chain 'B' and resid 483 through 491 Processing helix chain 'B' and resid 494 through 509 Processing helix chain 'C' and resid 65 through 79 Processing helix chain 'C' and resid 89 through 135 removed outlier: 3.501A pdb=" N ARG C 93 " --> pdb=" O SER C 89 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ASN C 135 " --> pdb=" O TYR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 340 Proline residue: C 326 - end of helix removed outlier: 4.037A pdb=" N GLY C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 424 through 438 Processing helix chain 'C' and resid 445 through 454 Processing helix chain 'C' and resid 469 through 483 removed outlier: 3.843A pdb=" N VAL C 481 " --> pdb=" O ALA C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 491 removed outlier: 3.838A pdb=" N HIS C 489 " --> pdb=" O GLU C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 509 removed outlier: 3.586A pdb=" N ARG C 500 " --> pdb=" O HIS C 496 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 401 through 406 removed outlier: 5.696A pdb=" N ILE A 364 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER A 463 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL A 366 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 410 through 414 Processing sheet with id=AA3, first strand: chain 'B' and resid 401 through 408 removed outlier: 6.666A pdb=" N ILE B 364 " --> pdb=" O SER B 463 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N SER B 463 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N VAL B 366 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 410 through 414 Processing sheet with id=AA5, first strand: chain 'C' and resid 401 through 406 removed outlier: 6.421A pdb=" N ILE C 364 " --> pdb=" O SER C 463 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER C 463 " --> pdb=" O ILE C 364 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL C 366 " --> pdb=" O LEU C 461 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 410 through 414 408 hydrogen bonds defined for protein. 1176 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: 1.67 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2085 1.34 - 1.46: 1019 1.46 - 1.58: 3022 1.58 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 6144 Sorted by residual: bond pdb=" CG LYS B 98 " pdb=" CD LYS B 98 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.30e+00 bond pdb=" CA GLN C 444 " pdb=" CB GLN C 444 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.69e-02 3.50e+03 1.08e+00 bond pdb=" CB GLU C 82 " pdb=" CG GLU C 82 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.31e-01 bond pdb=" CG GLU C 82 " pdb=" CD GLU C 82 " ideal model delta sigma weight residual 1.516 1.493 0.023 2.50e-02 1.60e+03 8.25e-01 bond pdb=" N GLN C 444 " pdb=" CA GLN C 444 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.29e-02 6.01e+03 7.98e-01 ... (remaining 6139 not shown) Histogram of bond angle deviations from ideal: 100.42 - 107.14: 166 107.14 - 113.85: 3438 113.85 - 120.57: 2461 120.57 - 127.29: 2208 127.29 - 134.00: 70 Bond angle restraints: 8343 Sorted by residual: angle pdb=" C THR C 443 " pdb=" N GLN C 444 " pdb=" CA GLN C 444 " ideal model delta sigma weight residual 121.54 129.05 -7.51 1.91e+00 2.74e-01 1.55e+01 angle pdb=" C THR B 443 " pdb=" N GLN B 444 " pdb=" CA GLN B 444 " ideal model delta sigma weight residual 121.54 128.76 -7.22 1.91e+00 2.74e-01 1.43e+01 angle pdb=" C HIS C 384 " pdb=" N HIS C 385 " pdb=" CA HIS C 385 " ideal model delta sigma weight residual 121.54 128.01 -6.47 1.91e+00 2.74e-01 1.15e+01 angle pdb=" CA LEU B 414 " pdb=" CB LEU B 414 " pdb=" CG LEU B 414 " ideal model delta sigma weight residual 116.30 126.29 -9.99 3.50e+00 8.16e-02 8.14e+00 angle pdb=" CA GLN C 444 " pdb=" CB GLN C 444 " pdb=" CG GLN C 444 " ideal model delta sigma weight residual 114.10 119.53 -5.43 2.00e+00 2.50e-01 7.36e+00 ... (remaining 8338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 3244 17.84 - 35.68: 311 35.68 - 53.52: 55 53.52 - 71.36: 10 71.36 - 89.19: 4 Dihedral angle restraints: 3624 sinusoidal: 1284 harmonic: 2340 Sorted by residual: dihedral pdb=" CA TYR C 65 " pdb=" C TYR C 65 " pdb=" N GLY C 66 " pdb=" CA GLY C 66 " ideal model delta harmonic sigma weight residual 180.00 -158.17 -21.83 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA HIS B 385 " pdb=" C HIS B 385 " pdb=" N HIS B 386 " pdb=" CA HIS B 386 " ideal model delta harmonic sigma weight residual 180.00 158.93 21.07 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA HIS A 385 " pdb=" C HIS A 385 " pdb=" N HIS A 386 " pdb=" CA HIS A 386 " ideal model delta harmonic sigma weight residual 180.00 163.30 16.70 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 3621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 584 0.035 - 0.070: 249 0.070 - 0.105: 70 0.105 - 0.139: 25 0.139 - 0.174: 2 Chirality restraints: 930 Sorted by residual: chirality pdb=" CB ILE B 399 " pdb=" CA ILE B 399 " pdb=" CG1 ILE B 399 " pdb=" CG2 ILE B 399 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA PRO A 370 " pdb=" N PRO A 370 " pdb=" C PRO A 370 " pdb=" CB PRO A 370 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CG LEU C 433 " pdb=" CB LEU C 433 " pdb=" CD1 LEU C 433 " pdb=" CD2 LEU C 433 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 927 not shown) Planarity restraints: 1107 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 89 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO C 90 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO C 90 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 90 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 89 " 0.023 5.00e-02 4.00e+02 3.53e-02 2.00e+00 pdb=" N PRO A 90 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 90 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 90 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 378 " -0.013 2.00e-02 2.50e+03 9.35e-03 1.53e+00 pdb=" CG PHE C 378 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE C 378 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE C 378 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 378 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 378 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 378 " -0.005 2.00e-02 2.50e+03 ... (remaining 1104 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1748 2.82 - 3.34: 5705 3.34 - 3.86: 9613 3.86 - 4.38: 10615 4.38 - 4.90: 18932 Nonbonded interactions: 46613 Sorted by model distance: nonbonded pdb=" O ALA B 369 " pdb=" OG SER B 373 " model vdw 2.298 2.440 nonbonded pdb=" O HIS A 384 " pdb=" ND1 HIS A 385 " model vdw 2.311 2.520 nonbonded pdb=" O HIS B 384 " pdb=" ND1 HIS B 385 " model vdw 2.317 2.520 nonbonded pdb=" O SER C 89 " pdb=" OG SER C 89 " model vdw 2.351 2.440 nonbonded pdb=" OD2 ASP C 86 " pdb=" NH2 ARG C 499 " model vdw 2.353 2.520 ... (remaining 46608 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.540 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: 0.030 Extract box with map and model: 5.960 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 20.830 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 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 : 0.004 0.045 6144 Z= 0.237 Angle : 0.631 9.986 8343 Z= 0.333 Chirality : 0.044 0.174 930 Planarity : 0.004 0.036 1107 Dihedral : 14.578 89.195 2112 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.31), residues: 798 helix: 1.96 (0.25), residues: 423 sheet: -0.01 (0.44), residues: 139 loop : -2.36 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 371 HIS 0.008 0.001 HIS B 489 PHE 0.020 0.002 PHE C 378 TYR 0.015 0.001 TYR A 367 ARG 0.003 0.000 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.694 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1748 time to fit residues: 26.9002 Evaluate side-chains 87 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 73 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6144 Z= 0.206 Angle : 0.555 8.234 8343 Z= 0.293 Chirality : 0.041 0.143 930 Planarity : 0.004 0.033 1107 Dihedral : 4.337 21.049 870 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.80 % Allowed : 11.35 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.31), residues: 798 helix: 2.18 (0.25), residues: 436 sheet: 0.11 (0.46), residues: 136 loop : -2.60 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 371 HIS 0.005 0.001 HIS B 489 PHE 0.020 0.002 PHE A 508 TYR 0.012 0.001 TYR A 367 ARG 0.002 0.000 ARG B 448 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.653 Fit side-chains REVERT: B 482 TYR cc_start: 0.7623 (OUTLIER) cc_final: 0.7235 (p90) outliers start: 10 outliers final: 6 residues processed: 89 average time/residue: 0.1541 time to fit residues: 18.9972 Evaluate side-chains 89 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 8.9990 chunk 22 optimal weight: 0.0370 chunk 61 optimal weight: 0.8980 chunk 50 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 73 optimal weight: 0.2980 chunk 79 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 25 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 overall best weight: 2.4462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6144 Z= 0.139 Angle : 0.500 8.140 8343 Z= 0.262 Chirality : 0.039 0.124 930 Planarity : 0.003 0.034 1107 Dihedral : 3.920 20.076 870 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.80 % Allowed : 13.15 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.31), residues: 798 helix: 2.50 (0.25), residues: 435 sheet: 0.30 (0.47), residues: 136 loop : -2.54 (0.37), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 371 HIS 0.003 0.001 HIS B 489 PHE 0.018 0.002 PHE C 378 TYR 0.017 0.001 TYR C 482 ARG 0.001 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.748 Fit side-chains REVERT: B 482 TYR cc_start: 0.7704 (OUTLIER) cc_final: 0.7231 (p90) REVERT: B 489 HIS cc_start: 0.8076 (OUTLIER) cc_final: 0.7818 (m-70) REVERT: C 372 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7237 (m-30) outliers start: 10 outliers final: 7 residues processed: 96 average time/residue: 0.1527 time to fit residues: 20.4220 Evaluate side-chains 90 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 HIS ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6144 Z= 0.285 Angle : 0.583 8.310 8343 Z= 0.308 Chirality : 0.042 0.143 930 Planarity : 0.004 0.031 1107 Dihedral : 4.534 21.690 870 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.42 % Allowed : 14.05 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.31), residues: 798 helix: 2.31 (0.25), residues: 433 sheet: -0.04 (0.45), residues: 142 loop : -2.48 (0.37), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 371 HIS 0.005 0.001 HIS B 489 PHE 0.021 0.002 PHE A 378 TYR 0.013 0.002 TYR B 367 ARG 0.003 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 0.741 Fit side-chains REVERT: B 482 TYR cc_start: 0.7848 (OUTLIER) cc_final: 0.7361 (p90) REVERT: C 103 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6587 (tm-30) outliers start: 19 outliers final: 12 residues processed: 93 average time/residue: 0.1496 time to fit residues: 19.2925 Evaluate side-chains 92 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 HIS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 512 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 chunk 54 optimal weight: 40.0000 chunk 0 optimal weight: 30.0000 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 30.0000 chunk 19 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 15 optimal weight: 0.0870 overall best weight: 4.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 HIS C 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6144 Z= 0.191 Angle : 0.535 8.105 8343 Z= 0.280 Chirality : 0.040 0.146 930 Planarity : 0.003 0.034 1107 Dihedral : 4.208 20.691 870 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.24 % Allowed : 14.77 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.31), residues: 798 helix: 2.47 (0.25), residues: 432 sheet: 0.09 (0.46), residues: 139 loop : -2.33 (0.38), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 371 HIS 0.004 0.001 HIS B 489 PHE 0.018 0.002 PHE A 378 TYR 0.011 0.001 TYR A 367 ARG 0.002 0.000 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 0.685 Fit side-chains REVERT: B 482 TYR cc_start: 0.7728 (OUTLIER) cc_final: 0.7223 (p90) REVERT: B 489 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.7905 (m170) REVERT: C 103 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6524 (tm-30) outliers start: 18 outliers final: 12 residues processed: 91 average time/residue: 0.1392 time to fit residues: 17.9593 Evaluate side-chains 89 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 74 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 HIS Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 65 optimal weight: 0.0060 chunk 36 optimal weight: 5.9990 chunk 6 optimal weight: 40.0000 chunk 25 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 75 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 overall best weight: 5.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6144 Z= 0.223 Angle : 0.548 8.062 8343 Z= 0.288 Chirality : 0.041 0.143 930 Planarity : 0.003 0.036 1107 Dihedral : 4.311 20.770 870 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.42 % Allowed : 15.14 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.31), residues: 798 helix: 2.41 (0.25), residues: 432 sheet: 0.24 (0.47), residues: 136 loop : -2.32 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 371 HIS 0.005 0.001 HIS B 489 PHE 0.018 0.002 PHE A 378 TYR 0.011 0.001 TYR A 367 ARG 0.001 0.000 ARG B 500 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 0.686 Fit side-chains REVERT: A 115 TYR cc_start: 0.3098 (OUTLIER) cc_final: 0.2760 (t80) REVERT: B 105 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6903 (tm-30) REVERT: B 482 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.7259 (p90) REVERT: B 489 HIS cc_start: 0.8270 (OUTLIER) cc_final: 0.8000 (m170) REVERT: C 103 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6640 (tm-30) outliers start: 19 outliers final: 14 residues processed: 94 average time/residue: 0.1417 time to fit residues: 18.8918 Evaluate side-chains 98 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 HIS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 48 optimal weight: 0.0070 chunk 47 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 23 optimal weight: 30.0000 overall best weight: 5.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 HIS ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6144 Z= 0.211 Angle : 0.545 8.002 8343 Z= 0.286 Chirality : 0.041 0.132 930 Planarity : 0.003 0.035 1107 Dihedral : 4.274 20.781 870 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.60 % Allowed : 15.50 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.31), residues: 798 helix: 2.46 (0.25), residues: 432 sheet: 0.22 (0.47), residues: 136 loop : -2.32 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 371 HIS 0.005 0.001 HIS B 489 PHE 0.018 0.002 PHE C 378 TYR 0.018 0.001 TYR A 466 ARG 0.001 0.000 ARG B 500 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 79 time to evaluate : 0.698 Fit side-chains REVERT: A 115 TYR cc_start: 0.2980 (OUTLIER) cc_final: 0.2703 (t80) REVERT: B 105 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6923 (tm-30) REVERT: B 482 TYR cc_start: 0.7736 (OUTLIER) cc_final: 0.7232 (p90) REVERT: B 489 HIS cc_start: 0.8277 (OUTLIER) cc_final: 0.7956 (m170) REVERT: C 103 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6611 (tm-30) outliers start: 20 outliers final: 13 residues processed: 93 average time/residue: 0.1435 time to fit residues: 18.8151 Evaluate side-chains 94 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 76 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 512 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 7 optimal weight: 40.0000 chunk 61 optimal weight: 0.8980 chunk 71 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 HIS ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 HIS ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6144 Z= 0.200 Angle : 0.539 7.963 8343 Z= 0.282 Chirality : 0.040 0.133 930 Planarity : 0.003 0.035 1107 Dihedral : 4.223 21.380 870 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.60 % Allowed : 15.86 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.31), residues: 798 helix: 2.52 (0.25), residues: 432 sheet: 0.24 (0.47), residues: 136 loop : -2.31 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 371 HIS 0.005 0.001 HIS B 489 PHE 0.018 0.002 PHE C 378 TYR 0.013 0.001 TYR A 466 ARG 0.001 0.000 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 78 time to evaluate : 0.683 Fit side-chains REVERT: A 115 TYR cc_start: 0.3216 (OUTLIER) cc_final: 0.2927 (t80) REVERT: B 105 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6879 (tm-30) REVERT: B 482 TYR cc_start: 0.7783 (OUTLIER) cc_final: 0.7289 (p90) REVERT: B 489 HIS cc_start: 0.8266 (OUTLIER) cc_final: 0.7996 (m170) REVERT: C 103 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6607 (tm-30) outliers start: 20 outliers final: 14 residues processed: 92 average time/residue: 0.1556 time to fit residues: 20.0210 Evaluate side-chains 98 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 512 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 68 optimal weight: 30.0000 chunk 72 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 HIS ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6144 Z= 0.270 Angle : 0.581 8.090 8343 Z= 0.305 Chirality : 0.042 0.138 930 Planarity : 0.004 0.035 1107 Dihedral : 4.524 24.385 870 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.42 % Allowed : 16.40 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.31), residues: 798 helix: 2.29 (0.25), residues: 435 sheet: 0.15 (0.47), residues: 136 loop : -2.23 (0.38), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 371 HIS 0.006 0.001 HIS B 489 PHE 0.019 0.002 PHE A 378 TYR 0.013 0.002 TYR A 466 ARG 0.002 0.000 ARG B 500 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 0.735 Fit side-chains REVERT: A 115 TYR cc_start: 0.4054 (OUTLIER) cc_final: 0.3251 (t80) REVERT: B 105 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6907 (tm-30) REVERT: B 482 TYR cc_start: 0.7945 (OUTLIER) cc_final: 0.7426 (p90) REVERT: B 489 HIS cc_start: 0.8371 (OUTLIER) cc_final: 0.8120 (m170) REVERT: C 103 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6676 (tm-30) outliers start: 19 outliers final: 13 residues processed: 92 average time/residue: 0.1424 time to fit residues: 18.5809 Evaluate side-chains 95 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 chunk 64 optimal weight: 30.0000 chunk 6 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 39 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 HIS ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6144 Z= 0.211 Angle : 0.552 7.966 8343 Z= 0.289 Chirality : 0.041 0.139 930 Planarity : 0.003 0.036 1107 Dihedral : 4.341 26.855 870 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.42 % Allowed : 16.40 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.31), residues: 798 helix: 2.44 (0.25), residues: 433 sheet: 0.21 (0.47), residues: 136 loop : -2.25 (0.38), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 371 HIS 0.005 0.001 HIS B 489 PHE 0.018 0.002 PHE C 378 TYR 0.011 0.001 TYR A 367 ARG 0.004 0.000 ARG B 423 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 0.697 Fit side-chains REVERT: A 115 TYR cc_start: 0.3568 (OUTLIER) cc_final: 0.2871 (t80) REVERT: B 105 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6879 (tm-30) REVERT: B 482 TYR cc_start: 0.7778 (OUTLIER) cc_final: 0.7314 (p90) REVERT: B 489 HIS cc_start: 0.8313 (OUTLIER) cc_final: 0.7972 (m170) REVERT: C 103 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6628 (tm-30) outliers start: 19 outliers final: 14 residues processed: 92 average time/residue: 0.1429 time to fit residues: 18.5951 Evaluate side-chains 99 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 482 TYR Chi-restraints excluded: chain B residue 489 HIS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 3.9990 chunk 64 optimal weight: 30.0000 chunk 26 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 56 optimal weight: 0.0370 chunk 3 optimal weight: 0.1980 chunk 46 optimal weight: 0.1980 chunk 73 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 overall best weight: 1.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 HIS ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.176030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.149980 restraints weight = 9482.418| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.05 r_work: 0.3568 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6144 Z= 0.133 Angle : 0.513 7.771 8343 Z= 0.264 Chirality : 0.039 0.147 930 Planarity : 0.003 0.038 1107 Dihedral : 3.900 28.250 870 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.88 % Allowed : 17.12 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.31), residues: 798 helix: 2.73 (0.24), residues: 433 sheet: 0.70 (0.50), residues: 127 loop : -2.34 (0.36), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 371 HIS 0.005 0.001 HIS C 385 PHE 0.019 0.002 PHE C 392 TYR 0.008 0.001 TYR A 367 ARG 0.005 0.000 ARG B 423 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1453.68 seconds wall clock time: 27 minutes 2.78 seconds (1622.78 seconds total)