Starting phenix.real_space_refine on Fri Aug 2 17:35:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v3r_42951/08_2024/8v3r_42951.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v3r_42951/08_2024/8v3r_42951.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/8v3r_42951/08_2024/8v3r_42951.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v3r_42951/08_2024/8v3r_42951.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v3r_42951/08_2024/8v3r_42951.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v3r_42951/08_2024/8v3r_42951.cif" } 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 23 5.16 5 C 2521 2.51 5 N 711 2.21 5 O 697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 4": "NH1" <-> "NH2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A ARG 204": "NH1" <-> "NH2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 223": "NH1" <-> "NH2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 250": "NH1" <-> "NH2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A ARG 281": "NH1" <-> "NH2" Residue "A ARG 282": "NH1" <-> "NH2" Residue "A ARG 299": "NH1" <-> "NH2" Residue "A ARG 303": "NH1" <-> "NH2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A ARG 341": "NH1" <-> "NH2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A ARG 500": "NH1" <-> "NH2" Residue "A ARG 523": "NH1" <-> "NH2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A ARG 549": "NH1" <-> "NH2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A ARG 590": "NH1" <-> "NH2" Residue "A ARG 598": "NH1" <-> "NH2" Residue "A ARG 601": "NH1" <-> "NH2" Residue "M GLU 1001": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3953 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3914 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 35, 'TRANS': 465} Chain breaks: 3 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 105 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 14, 'ARG:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 109 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1, 'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 5.12, per 1000 atoms: 1.30 Number of scatterers: 3953 At special positions: 0 Unit cell: (80.925, 77.19, 72.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 23 16.00 O 697 8.00 N 711 7.00 C 2521 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 700.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" ND1 HIS A 252 " pdb="ZN ZN A 701 " - pdb=" ND1 HIS A 434 " 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 952 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 4 sheets defined 31.4% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 98 through 104 Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 256 through 270 removed outlier: 3.910A pdb=" N PHE A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 323 through 340 Processing helix chain 'A' and resid 451 through 467 removed outlier: 4.340A pdb=" N TYR A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) Proline residue: A 462 - end of helix Processing helix chain 'A' and resid 481 through 486 removed outlier: 3.890A pdb=" N TYR A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 497 removed outlier: 3.668A pdb=" N GLY A 497 " --> pdb=" O SER A 494 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 494 through 497' Processing helix chain 'A' and resid 498 through 508 Processing helix chain 'A' and resid 551 through 570 removed outlier: 3.505A pdb=" N MET A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 585 through 601 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 removed outlier: 6.747A pdb=" N VAL A 110 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG A 118 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 24 removed outlier: 6.471A pdb=" N TYR A 52 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ASN A 91 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE A 54 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 198 removed outlier: 7.159A pdb=" N VAL A 205 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE A 245 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ILE A 289 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU A 247 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR A 429 " --> pdb=" O ILE A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 216 through 220 removed outlier: 5.426A pdb=" N ARG A 238 " --> pdb=" O ARG A 217 " (cutoff:3.500A) 154 hydrogen bonds defined for protein. 432 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: 1.17 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 724 1.31 - 1.44: 1095 1.44 - 1.57: 2207 1.57 - 1.69: 4 1.69 - 1.82: 35 Bond restraints: 4065 Sorted by residual: bond pdb=" CD2 HIS A 436 " pdb=" NE2 HIS A 436 " ideal model delta sigma weight residual 1.374 1.331 0.043 1.10e-02 8.26e+03 1.56e+01 bond pdb=" CZ ARG A 303 " pdb=" NH2 ARG A 303 " ideal model delta sigma weight residual 1.330 1.280 0.050 1.30e-02 5.92e+03 1.50e+01 bond pdb=" CZ ARG A 303 " pdb=" NH1 ARG A 303 " ideal model delta sigma weight residual 1.323 1.274 0.049 1.40e-02 5.10e+03 1.21e+01 bond pdb=" CZ ARG A 220 " pdb=" NH2 ARG A 220 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.03e+01 bond pdb=" CZ ARG A 299 " pdb=" NH2 ARG A 299 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 1.00e+01 ... (remaining 4060 not shown) Histogram of bond angle deviations from ideal: 98.76 - 105.83: 156 105.83 - 112.91: 1944 112.91 - 119.99: 1558 119.99 - 127.07: 1810 127.07 - 134.14: 53 Bond angle restraints: 5521 Sorted by residual: angle pdb=" N PRO A 542 " pdb=" CA PRO A 542 " pdb=" CB PRO A 542 " ideal model delta sigma weight residual 103.19 106.12 -2.93 5.60e-01 3.19e+00 2.75e+01 angle pdb=" OD1 ASN A 518 " pdb=" CG ASN A 518 " pdb=" ND2 ASN A 518 " ideal model delta sigma weight residual 122.60 117.43 5.17 1.00e+00 1.00e+00 2.67e+01 angle pdb=" OE1 GLN A 134 " pdb=" CD GLN A 134 " pdb=" NE2 GLN A 134 " ideal model delta sigma weight residual 122.60 117.72 4.88 1.00e+00 1.00e+00 2.38e+01 angle pdb=" CA ASN A 478 " pdb=" CB ASN A 478 " pdb=" CG ASN A 478 " ideal model delta sigma weight residual 112.60 117.33 -4.73 1.00e+00 1.00e+00 2.24e+01 angle pdb=" CB HIS A 434 " pdb=" CG HIS A 434 " pdb=" CD2 HIS A 434 " ideal model delta sigma weight residual 131.20 125.36 5.84 1.30e+00 5.92e-01 2.02e+01 ... (remaining 5516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 2240 17.77 - 35.54: 130 35.54 - 53.31: 25 53.31 - 71.07: 6 71.07 - 88.84: 3 Dihedral angle restraints: 2404 sinusoidal: 930 harmonic: 1474 Sorted by residual: dihedral pdb=" CA THR A 112 " pdb=" C THR A 112 " pdb=" N LEU A 113 " pdb=" CA LEU A 113 " ideal model delta harmonic sigma weight residual 180.00 -159.14 -20.86 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA TYR A 429 " pdb=" C TYR A 429 " pdb=" N TYR A 430 " pdb=" CA TYR A 430 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA HIS A 583 " pdb=" C HIS A 583 " pdb=" N SER A 584 " pdb=" CA SER A 584 " ideal model delta harmonic sigma weight residual -180.00 -161.44 -18.56 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 2401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 376 0.073 - 0.147: 158 0.147 - 0.220: 49 0.220 - 0.293: 5 0.293 - 0.367: 1 Chirality restraints: 589 Sorted by residual: chirality pdb=" CA SER A 16 " pdb=" N SER A 16 " pdb=" C SER A 16 " pdb=" CB SER A 16 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA GLU M1001 " pdb=" N GLU M1001 " pdb=" C GLU M1001 " pdb=" CB GLU M1001 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA ASN A 293 " pdb=" N ASN A 293 " pdb=" C ASN A 293 " pdb=" CB ASN A 293 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 586 not shown) Planarity restraints: 723 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 192 " -0.063 2.00e-02 2.50e+03 4.72e-02 3.34e+01 pdb=" CG HIS A 192 " 0.072 2.00e-02 2.50e+03 pdb=" ND1 HIS A 192 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 HIS A 192 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 HIS A 192 " -0.021 2.00e-02 2.50e+03 pdb=" NE2 HIS A 192 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 575 " 0.055 2.00e-02 2.50e+03 3.32e-02 2.76e+01 pdb=" CG TRP A 575 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP A 575 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TRP A 575 " -0.012 2.00e-02 2.50e+03 pdb=" NE1 TRP A 575 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TRP A 575 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 575 " -0.042 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 575 " 0.041 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 575 " -0.029 2.00e-02 2.50e+03 pdb=" CH2 TRP A 575 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 335 " -0.067 2.00e-02 2.50e+03 3.59e-02 2.58e+01 pdb=" CG TYR A 335 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 335 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR A 335 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR A 335 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 335 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 335 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 335 " -0.052 2.00e-02 2.50e+03 ... (remaining 720 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.09: 2 2.09 - 2.79: 611 2.79 - 3.49: 5567 3.49 - 4.20: 9535 4.20 - 4.90: 16732 Nonbonded interactions: 32447 Sorted by model distance: nonbonded pdb=" CD GLU M 3 " pdb=" N GLU M1001 " model vdw 1.385 3.350 nonbonded pdb=" OE2 GLU A 255 " pdb="ZN ZN A 701 " model vdw 1.701 2.230 nonbonded pdb=" NH2 ARG A 500 " pdb=" OE1 GLU M1001 " model vdw 2.236 3.120 nonbonded pdb=" OE1 GLU M 3 " pdb=" N GLU M1001 " model vdw 2.292 3.120 nonbonded pdb=" ND2 ASN A 312 " pdb=" O GLU M1001 " model vdw 2.366 3.120 ... (remaining 32442 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.740 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 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 : 0.012 0.063 4065 Z= 0.808 Angle : 1.582 7.220 5521 Z= 1.060 Chirality : 0.086 0.367 589 Planarity : 0.012 0.081 723 Dihedral : 12.459 88.842 1452 Min Nonbonded Distance : 1.385 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.24 % Allowed : 5.10 % Favored : 94.66 % 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: -0.46 (0.36), residues: 493 helix: 0.21 (0.39), residues: 142 sheet: 0.20 (0.55), residues: 85 loop : -0.72 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.016 TRP A 575 HIS 0.016 0.004 HIS A 436 PHE 0.047 0.009 PHE A 265 TYR 0.067 0.014 TYR A 335 ARG 0.008 0.001 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 65 THR cc_start: 0.7815 (m) cc_final: 0.7499 (p) REVERT: A 68 GLU cc_start: 0.8535 (tt0) cc_final: 0.7961 (tt0) REVERT: A 93 MET cc_start: 0.7871 (mmm) cc_final: 0.7337 (mmm) REVERT: A 170 GLN cc_start: 0.6808 (mt0) cc_final: 0.6393 (mt0) REVERT: A 173 GLN cc_start: 0.7202 (mm110) cc_final: 0.6452 (pt0) REVERT: A 204 ARG cc_start: 0.8389 (mtp-110) cc_final: 0.8062 (mtp-110) REVERT: A 206 ASP cc_start: 0.7226 (t0) cc_final: 0.6843 (p0) REVERT: A 314 GLN cc_start: 0.8551 (mm110) cc_final: 0.8173 (mm110) REVERT: A 316 LEU cc_start: 0.9105 (mt) cc_final: 0.8498 (mt) REVERT: A 322 LEU cc_start: 0.8684 (mp) cc_final: 0.8340 (mt) REVERT: A 440 ARG cc_start: 0.7842 (mtm110) cc_final: 0.6529 (mtp180) REVERT: A 483 ASN cc_start: 0.7222 (t0) cc_final: 0.6603 (t0) REVERT: A 523 ARG cc_start: 0.8093 (mtm110) cc_final: 0.7204 (ttm-80) REVERT: A 534 ASP cc_start: 0.8472 (p0) cc_final: 0.7935 (p0) REVERT: A 562 MET cc_start: 0.7820 (mtp) cc_final: 0.7578 (mtm) REVERT: A 598 ARG cc_start: 0.6705 (mmm160) cc_final: 0.6099 (mtm180) outliers start: 1 outliers final: 1 residues processed: 98 average time/residue: 0.2321 time to fit residues: 26.6775 Evaluate side-chains 63 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 3 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.0970 chunk 37 optimal weight: 0.1980 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.1980 chunk 25 optimal weight: 0.0270 chunk 20 optimal weight: 0.2980 chunk 39 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 23 optimal weight: 0.0870 chunk 29 optimal weight: 0.4980 chunk 45 optimal weight: 0.2980 overall best weight: 0.1214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4065 Z= 0.202 Angle : 0.594 9.406 5521 Z= 0.308 Chirality : 0.041 0.136 589 Planarity : 0.005 0.048 723 Dihedral : 4.795 20.614 563 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.43 % Allowed : 10.19 % Favored : 87.38 % 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: 0.40 (0.37), residues: 493 helix: 1.33 (0.41), residues: 143 sheet: 0.45 (0.52), residues: 93 loop : -0.37 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 57 HIS 0.004 0.001 HIS A 192 PHE 0.016 0.002 PHE A 153 TYR 0.013 0.002 TYR A 335 ARG 0.005 0.001 ARG A 590 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 0.465 Fit side-chains REVERT: A 65 THR cc_start: 0.7682 (m) cc_final: 0.7357 (p) REVERT: A 68 GLU cc_start: 0.8604 (tt0) cc_final: 0.8035 (tt0) REVERT: A 173 GLN cc_start: 0.7129 (mm110) cc_final: 0.6408 (pt0) REVERT: A 267 ASP cc_start: 0.6994 (m-30) cc_final: 0.6721 (m-30) REVERT: A 316 LEU cc_start: 0.9096 (mt) cc_final: 0.8465 (mt) REVERT: A 459 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7890 (ttm) REVERT: A 483 ASN cc_start: 0.6952 (t0) cc_final: 0.6296 (t0) REVERT: A 523 ARG cc_start: 0.7967 (mtm110) cc_final: 0.7581 (ttp-110) REVERT: A 534 ASP cc_start: 0.8447 (p0) cc_final: 0.8057 (p0) REVERT: A 598 ARG cc_start: 0.6889 (mmm160) cc_final: 0.6094 (mtm180) outliers start: 10 outliers final: 5 residues processed: 71 average time/residue: 0.1868 time to fit residues: 16.3259 Evaluate side-chains 58 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 599 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 0.0980 chunk 12 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 49 optimal weight: 0.1980 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 0.2980 chunk 36 optimal weight: 0.0870 chunk 44 optimal weight: 0.4980 overall best weight: 0.2358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS A 599 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4065 Z= 0.278 Angle : 0.590 8.722 5521 Z= 0.302 Chirality : 0.042 0.126 589 Planarity : 0.005 0.039 723 Dihedral : 4.690 17.396 560 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.64 % Allowed : 11.17 % Favored : 85.19 % 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: 0.46 (0.38), residues: 493 helix: 1.32 (0.42), residues: 144 sheet: 0.62 (0.54), residues: 93 loop : -0.36 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 119 HIS 0.004 0.001 HIS A 192 PHE 0.018 0.002 PHE A 245 TYR 0.017 0.002 TYR A 519 ARG 0.004 0.001 ARG A 590 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 54 time to evaluate : 0.456 Fit side-chains REVERT: A 65 THR cc_start: 0.8056 (m) cc_final: 0.7729 (p) REVERT: A 93 MET cc_start: 0.8111 (mmm) cc_final: 0.7813 (mmm) REVERT: A 173 GLN cc_start: 0.7193 (mm110) cc_final: 0.6612 (pt0) REVERT: A 267 ASP cc_start: 0.7011 (m-30) cc_final: 0.6753 (m-30) REVERT: A 316 LEU cc_start: 0.9133 (mt) cc_final: 0.8378 (mt) REVERT: A 483 ASN cc_start: 0.6882 (t0) cc_final: 0.6367 (t0) REVERT: A 523 ARG cc_start: 0.8077 (mtm110) cc_final: 0.7764 (ttp-110) REVERT: A 534 ASP cc_start: 0.8432 (p0) cc_final: 0.7966 (p0) REVERT: A 598 ARG cc_start: 0.6857 (mmm160) cc_final: 0.6087 (mtm180) outliers start: 15 outliers final: 10 residues processed: 64 average time/residue: 0.1580 time to fit residues: 12.9103 Evaluate side-chains 58 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 599 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 5 optimal weight: 0.0970 chunk 21 optimal weight: 0.1980 chunk 30 optimal weight: 0.1980 chunk 45 optimal weight: 0.2980 chunk 48 optimal weight: 0.0980 chunk 43 optimal weight: 0.7980 chunk 13 optimal weight: 0.0770 chunk 40 optimal weight: 0.9990 chunk 27 optimal weight: 0.0870 overall best weight: 0.1114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4065 Z= 0.190 Angle : 0.538 7.977 5521 Z= 0.272 Chirality : 0.040 0.134 589 Planarity : 0.004 0.035 723 Dihedral : 4.477 17.154 560 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.94 % Allowed : 13.83 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.38), residues: 493 helix: 1.43 (0.42), residues: 144 sheet: 0.69 (0.54), residues: 93 loop : -0.30 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 592 HIS 0.003 0.001 HIS A 192 PHE 0.016 0.002 PHE A 546 TYR 0.011 0.001 TYR A 519 ARG 0.002 0.000 ARG A 590 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.469 Fit side-chains REVERT: A 65 THR cc_start: 0.8076 (m) cc_final: 0.7752 (p) REVERT: A 68 GLU cc_start: 0.8679 (tt0) cc_final: 0.8233 (tt0) REVERT: A 93 MET cc_start: 0.8264 (mmm) cc_final: 0.8011 (mmm) REVERT: A 173 GLN cc_start: 0.7124 (mm110) cc_final: 0.6607 (pt0) REVERT: A 267 ASP cc_start: 0.6998 (m-30) cc_final: 0.6735 (m-30) REVERT: A 316 LEU cc_start: 0.9075 (mt) cc_final: 0.8289 (mt) REVERT: A 459 MET cc_start: 0.8059 (ttm) cc_final: 0.7751 (ttm) REVERT: A 483 ASN cc_start: 0.6836 (t0) cc_final: 0.6330 (t0) REVERT: A 519 TYR cc_start: 0.8443 (m-80) cc_final: 0.7329 (m-80) REVERT: A 523 ARG cc_start: 0.8041 (mtm110) cc_final: 0.7734 (ttp-110) REVERT: A 534 ASP cc_start: 0.8425 (p0) cc_final: 0.8029 (p0) REVERT: A 598 ARG cc_start: 0.6757 (mmm160) cc_final: 0.6081 (mtm180) outliers start: 8 outliers final: 6 residues processed: 60 average time/residue: 0.1869 time to fit residues: 14.0656 Evaluate side-chains 57 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 466 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 33 optimal weight: 0.0980 chunk 24 optimal weight: 0.0980 chunk 43 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 0.2980 chunk 28 optimal weight: 0.5980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 226 GLN A 599 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 4065 Z= 0.381 Angle : 0.631 9.013 5521 Z= 0.318 Chirality : 0.043 0.156 589 Planarity : 0.005 0.030 723 Dihedral : 4.728 17.928 560 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.64 % Allowed : 12.38 % Favored : 83.98 % 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: 0.19 (0.38), residues: 493 helix: 0.96 (0.41), residues: 144 sheet: 0.58 (0.53), residues: 99 loop : -0.51 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 119 HIS 0.004 0.001 HIS A 471 PHE 0.018 0.002 PHE A 245 TYR 0.019 0.002 TYR A 519 ARG 0.005 0.001 ARG A 590 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 43 time to evaluate : 0.475 Fit side-chains REVERT: A 93 MET cc_start: 0.8248 (mmm) cc_final: 0.8002 (mmm) REVERT: A 173 GLN cc_start: 0.7082 (mm110) cc_final: 0.6699 (pt0) REVERT: A 483 ASN cc_start: 0.6846 (t0) cc_final: 0.6354 (t0) REVERT: A 523 ARG cc_start: 0.8124 (mtm110) cc_final: 0.7782 (ttp-110) REVERT: A 556 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: A 598 ARG cc_start: 0.7000 (mmm160) cc_final: 0.6255 (mtm180) outliers start: 15 outliers final: 13 residues processed: 56 average time/residue: 0.1692 time to fit residues: 12.0018 Evaluate side-chains 58 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 44 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 599 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.5980 chunk 48 optimal weight: 0.1980 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 0.0770 chunk 4 optimal weight: 0.0870 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 0.0980 chunk 46 optimal weight: 0.0170 chunk 5 optimal weight: 0.0980 chunk 27 optimal weight: 0.0980 chunk 35 optimal weight: 0.3980 overall best weight: 0.0754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4065 Z= 0.165 Angle : 0.536 8.200 5521 Z= 0.269 Chirality : 0.040 0.141 589 Planarity : 0.004 0.031 723 Dihedral : 4.457 17.446 560 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.43 % Allowed : 14.32 % Favored : 83.25 % 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: 0.44 (0.38), residues: 493 helix: 1.30 (0.42), residues: 144 sheet: 0.65 (0.54), residues: 99 loop : -0.41 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 592 HIS 0.002 0.001 HIS A 192 PHE 0.012 0.002 PHE A 546 TYR 0.010 0.001 TYR A 335 ARG 0.004 0.000 ARG A 598 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 0.496 Fit side-chains REVERT: A 93 MET cc_start: 0.8065 (mmm) cc_final: 0.7506 (mmm) REVERT: A 173 GLN cc_start: 0.7205 (mm110) cc_final: 0.6855 (pt0) REVERT: A 483 ASN cc_start: 0.6831 (t0) cc_final: 0.6341 (t0) REVERT: A 519 TYR cc_start: 0.8505 (m-80) cc_final: 0.7427 (m-80) REVERT: A 523 ARG cc_start: 0.8109 (mtm110) cc_final: 0.7829 (ttp-110) REVERT: A 556 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7792 (mp0) REVERT: A 598 ARG cc_start: 0.6903 (mmm160) cc_final: 0.6206 (mtm180) outliers start: 10 outliers final: 7 residues processed: 53 average time/residue: 0.1994 time to fit residues: 13.0763 Evaluate side-chains 53 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 599 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.0170 chunk 40 optimal weight: 0.1980 chunk 48 optimal weight: 0.0870 chunk 30 optimal weight: 0.3980 chunk 29 optimal weight: 0.0980 chunk 22 optimal weight: 0.0870 chunk 19 optimal weight: 0.3980 chunk 28 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 overall best weight: 0.0974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4065 Z= 0.177 Angle : 0.539 8.976 5521 Z= 0.267 Chirality : 0.039 0.134 589 Planarity : 0.004 0.031 723 Dihedral : 4.357 16.705 560 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.67 % Allowed : 15.05 % Favored : 82.28 % 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: 0.52 (0.39), residues: 493 helix: 1.38 (0.43), residues: 144 sheet: 0.75 (0.54), residues: 99 loop : -0.40 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 592 HIS 0.002 0.001 HIS A 192 PHE 0.011 0.001 PHE A 153 TYR 0.009 0.001 TYR A 157 ARG 0.004 0.000 ARG A 590 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 44 time to evaluate : 0.499 Fit side-chains REVERT: A 93 MET cc_start: 0.8128 (mmm) cc_final: 0.7635 (mmm) REVERT: A 173 GLN cc_start: 0.7228 (mm110) cc_final: 0.6899 (pt0) REVERT: A 483 ASN cc_start: 0.6804 (t0) cc_final: 0.6315 (t0) REVERT: A 519 TYR cc_start: 0.8400 (m-80) cc_final: 0.7030 (m-80) REVERT: A 523 ARG cc_start: 0.8118 (mtm110) cc_final: 0.7840 (ttp-110) REVERT: A 556 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7770 (mp0) REVERT: A 598 ARG cc_start: 0.6920 (mmm160) cc_final: 0.6168 (mtm180) outliers start: 11 outliers final: 7 residues processed: 53 average time/residue: 0.1857 time to fit residues: 12.4091 Evaluate side-chains 51 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 599 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.3980 chunk 4 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 chunk 43 optimal weight: 0.0870 chunk 46 optimal weight: 0.1980 chunk 42 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 0.0470 chunk 19 optimal weight: 0.0170 chunk 35 optimal weight: 0.5980 chunk 13 optimal weight: 0.2980 overall best weight: 0.1294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 GLN A 599 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4065 Z= 0.188 Angle : 0.525 8.194 5521 Z= 0.262 Chirality : 0.039 0.132 589 Planarity : 0.004 0.030 723 Dihedral : 4.301 16.576 560 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.91 % Allowed : 14.81 % Favored : 82.28 % 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: 0.53 (0.39), residues: 493 helix: 1.46 (0.43), residues: 144 sheet: 0.73 (0.54), residues: 99 loop : -0.42 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 592 HIS 0.002 0.001 HIS A 583 PHE 0.011 0.001 PHE A 153 TYR 0.009 0.001 TYR A 519 ARG 0.004 0.000 ARG A 590 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 46 time to evaluate : 0.447 Fit side-chains REVERT: A 93 MET cc_start: 0.8131 (mmm) cc_final: 0.7634 (mmm) REVERT: A 104 GLN cc_start: 0.7687 (mt0) cc_final: 0.7436 (mt0) REVERT: A 173 GLN cc_start: 0.7197 (mm110) cc_final: 0.6915 (pt0) REVERT: A 322 LEU cc_start: 0.8698 (mp) cc_final: 0.8138 (mt) REVERT: A 440 ARG cc_start: 0.7043 (mtm110) cc_final: 0.6173 (mtp180) REVERT: A 483 ASN cc_start: 0.6760 (t0) cc_final: 0.6262 (t0) REVERT: A 519 TYR cc_start: 0.8388 (m-80) cc_final: 0.7065 (m-80) REVERT: A 523 ARG cc_start: 0.8087 (mtm110) cc_final: 0.7809 (ttp-110) REVERT: A 556 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7787 (mp0) REVERT: A 598 ARG cc_start: 0.6939 (mmm160) cc_final: 0.6298 (mtm180) outliers start: 12 outliers final: 7 residues processed: 56 average time/residue: 0.1926 time to fit residues: 13.5003 Evaluate side-chains 54 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 599 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.6980 chunk 42 optimal weight: 0.0570 chunk 44 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 47 optimal weight: 0.0770 chunk 28 optimal weight: 0.1980 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 0.0870 chunk 49 optimal weight: 0.0040 chunk 45 optimal weight: 0.4980 chunk 39 optimal weight: 0.4980 overall best weight: 0.0846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4065 Z= 0.160 Angle : 0.528 8.333 5521 Z= 0.261 Chirality : 0.039 0.130 589 Planarity : 0.004 0.030 723 Dihedral : 4.256 16.695 560 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.43 % Allowed : 15.05 % 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: 0.58 (0.39), residues: 493 helix: 1.52 (0.43), residues: 144 sheet: 0.76 (0.54), residues: 99 loop : -0.41 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 592 HIS 0.002 0.001 HIS A 471 PHE 0.011 0.001 PHE A 153 TYR 0.009 0.001 TYR A 157 ARG 0.006 0.000 ARG A 598 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.496 Fit side-chains REVERT: A 93 MET cc_start: 0.8126 (mmm) cc_final: 0.7896 (mmm) REVERT: A 104 GLN cc_start: 0.7680 (mt0) cc_final: 0.7385 (mt0) REVERT: A 173 GLN cc_start: 0.7184 (mm110) cc_final: 0.6917 (pt0) REVERT: A 322 LEU cc_start: 0.8670 (mp) cc_final: 0.8177 (mt) REVERT: A 440 ARG cc_start: 0.7022 (mtm110) cc_final: 0.5988 (mtp180) REVERT: A 483 ASN cc_start: 0.6732 (t0) cc_final: 0.6235 (t0) REVERT: A 519 TYR cc_start: 0.8336 (m-80) cc_final: 0.6956 (m-80) REVERT: A 523 ARG cc_start: 0.7994 (mtm110) cc_final: 0.7160 (ttm-80) REVERT: A 556 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7786 (mp0) REVERT: A 598 ARG cc_start: 0.6879 (mmm160) cc_final: 0.6170 (mtm180) outliers start: 10 outliers final: 7 residues processed: 58 average time/residue: 0.1936 time to fit residues: 13.9751 Evaluate side-chains 57 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 599 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 0.0370 chunk 31 optimal weight: 0.7980 chunk 42 optimal weight: 0.4980 chunk 12 optimal weight: 0.0970 chunk 36 optimal weight: 0.0980 chunk 5 optimal weight: 0.0970 chunk 11 optimal weight: 0.1980 chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.1054 ------------------------------------------------------------------------------- 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: 0.7349 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4065 Z= 0.171 Angle : 0.533 8.365 5521 Z= 0.265 Chirality : 0.039 0.129 589 Planarity : 0.004 0.030 723 Dihedral : 4.238 16.784 560 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.94 % Allowed : 16.02 % Favored : 82.04 % 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 (0.39), residues: 493 helix: 1.51 (0.43), residues: 144 sheet: 0.80 (0.54), residues: 99 loop : -0.40 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 592 HIS 0.002 0.001 HIS A 471 PHE 0.011 0.001 PHE A 265 TYR 0.009 0.001 TYR A 519 ARG 0.003 0.000 ARG A 590 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.468 Fit side-chains REVERT: A 93 MET cc_start: 0.8126 (mmm) cc_final: 0.7892 (mmm) REVERT: A 104 GLN cc_start: 0.7761 (mt0) cc_final: 0.7455 (mt0) REVERT: A 322 LEU cc_start: 0.8671 (mp) cc_final: 0.8187 (mt) REVERT: A 440 ARG cc_start: 0.7019 (mtm110) cc_final: 0.6003 (mtp180) REVERT: A 483 ASN cc_start: 0.6712 (t0) cc_final: 0.6219 (t0) REVERT: A 519 TYR cc_start: 0.8344 (m-80) cc_final: 0.6966 (m-80) REVERT: A 523 ARG cc_start: 0.7950 (mtm110) cc_final: 0.7101 (ttm-80) REVERT: A 556 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7783 (mp0) REVERT: A 598 ARG cc_start: 0.6935 (mmm160) cc_final: 0.6170 (mtm180) outliers start: 8 outliers final: 6 residues processed: 54 average time/residue: 0.1954 time to fit residues: 13.1236 Evaluate side-chains 54 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 556 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 chunk 26 optimal weight: 0.0770 chunk 1 optimal weight: 0.3980 chunk 31 optimal weight: 0.0870 chunk 30 optimal weight: 0.1980 overall best weight: 0.2316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 GLN A 599 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.118000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.107169 restraints weight = 5693.937| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.27 r_work: 0.3115 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4065 Z= 0.270 Angle : 0.568 8.884 5521 Z= 0.285 Chirality : 0.041 0.133 589 Planarity : 0.004 0.028 723 Dihedral : 4.413 17.233 560 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.43 % Allowed : 15.78 % Favored : 81.80 % 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: 0.54 (0.39), residues: 493 helix: 1.36 (0.43), residues: 144 sheet: 0.88 (0.55), residues: 99 loop : -0.42 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 592 HIS 0.003 0.001 HIS A 583 PHE 0.013 0.002 PHE A 245 TYR 0.013 0.002 TYR A 519 ARG 0.004 0.000 ARG A 590 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1603.65 seconds wall clock time: 28 minutes 59.22 seconds (1739.22 seconds total)