Starting phenix.real_space_refine on Fri Mar 15 06:27:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wnx_32634/03_2024/7wnx_32634_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wnx_32634/03_2024/7wnx_32634.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wnx_32634/03_2024/7wnx_32634_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wnx_32634/03_2024/7wnx_32634_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wnx_32634/03_2024/7wnx_32634_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wnx_32634/03_2024/7wnx_32634.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wnx_32634/03_2024/7wnx_32634.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wnx_32634/03_2024/7wnx_32634_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wnx_32634/03_2024/7wnx_32634_updated.pdb" } resolution = 3.36 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= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5250 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 28 5.16 5 Cl 1 4.86 5 C 3654 2.51 5 N 933 2.21 5 O 1025 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 7": "NH1" <-> "NH2" Residue "A PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 45": "OD1" <-> "OD2" Residue "A ASP 58": "OD1" <-> "OD2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 65": "NH1" <-> "NH2" Residue "A ASP 83": "OD1" <-> "OD2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ASP 145": "OD1" <-> "OD2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A ASP 185": "OD1" <-> "OD2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 256": "OD1" <-> "OD2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A ARG 281": "NH1" <-> "NH2" Residue "A ARG 288": "NH1" <-> "NH2" Residue "A ARG 344": "NH1" <-> "NH2" Residue "A GLU 384": "OE1" <-> "OE2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A ASP 476": "OD1" <-> "OD2" Residue "A ARG 523": "NH1" <-> "NH2" Residue "A ASP 531": "OD1" <-> "OD2" Residue "A ASP 555": "OD1" <-> "OD2" Residue "A ASP 562": "OD1" <-> "OD2" Residue "A PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 647": "OE1" <-> "OE2" Residue "A ARG 658": "NH1" <-> "NH2" Residue "A GLU 659": "OE1" <-> "OE2" Residue "A GLU 666": "OE1" <-> "OE2" Residue "A TYR 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 720": "NH1" <-> "NH2" Residue "A ASP 733": "OD1" <-> "OD2" Residue "A ASP 734": "OD1" <-> "OD2" Residue "A ARG 740": "NH1" <-> "NH2" Residue "A ARG 744": "NH1" <-> "NH2" Residue "A GLU 747": "OE1" <-> "OE2" Residue "A GLU 755": "OE1" <-> "OE2" Residue "A ARG 760": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5643 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5643 Unusual residues: {'1I2': 1} Classifications: {'peptide': 734, 'undetermined': 1} Link IDs: {'PTRANS': 37, 'TRANS': 696, None: 1} Not linked: pdbres="ARG A 760 " pdbres="1I2 A1101 " Chain breaks: 1 Time building chain proxies: 3.47, per 1000 atoms: 0.61 Number of scatterers: 5643 At special positions: 0 Unit cell: (77.08, 77.9, 115.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 28 16.00 F 2 9.00 O 1025 8.00 N 933 7.00 C 3654 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: 2.05 Conformation dependent library (CDL) restraints added in 1.1 seconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1344 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 1 sheets defined 63.9% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid -1 through 11 Processing helix chain 'A' and resid 15 through 31 Processing helix chain 'A' and resid 49 through 60 Processing helix chain 'A' and resid 84 through 100 Processing helix chain 'A' and resid 122 through 124 No H-bonds generated for 'chain 'A' and resid 122 through 124' Processing helix chain 'A' and resid 144 through 159 Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 172 through 205 Proline residue: A 195 - end of helix Processing helix chain 'A' and resid 209 through 235 Proline residue: A 214 - end of helix removed outlier: 4.195A pdb=" N GLU A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N PHE A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 268 removed outlier: 3.841A pdb=" N GLN A 243 " --> pdb=" O PHE A 240 " (cutoff:3.500A) Proline residue: A 244 - end of helix removed outlier: 3.997A pdb=" N GLY A 250 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLY A 252 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ILE A 253 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ALA A 254 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 255 " --> pdb=" O GLY A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 306 Proline residue: A 303 - end of helix removed outlier: 4.961A pdb=" N LEU A 306 " --> pdb=" O VAL A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 345 removed outlier: 4.082A pdb=" N SER A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 384 through 398 Processing helix chain 'A' and resid 402 through 414 Proline residue: A 407 - end of helix Processing helix chain 'A' and resid 417 through 420 Processing helix chain 'A' and resid 437 through 448 Processing helix chain 'A' and resid 473 through 483 removed outlier: 4.256A pdb=" N THR A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 526 through 535 Processing helix chain 'A' and resid 549 through 582 Proline residue: A 565 - end of helix removed outlier: 3.903A pdb=" N ALA A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 611 removed outlier: 3.945A pdb=" N ILE A 590 " --> pdb=" O VAL A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 620 No H-bonds generated for 'chain 'A' and resid 617 through 620' Processing helix chain 'A' and resid 629 through 658 removed outlier: 3.964A pdb=" N ILE A 632 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLY A 633 " --> pdb=" O PRO A 630 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE A 635 " --> pdb=" O ILE A 632 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TRP A 640 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR A 646 " --> pdb=" O SER A 643 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU A 647 " --> pdb=" O THR A 644 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL A 651 " --> pdb=" O VAL A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 694 removed outlier: 4.844A pdb=" N ARG A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 730 removed outlier: 3.630A pdb=" N ILE A 718 " --> pdb=" O LEU A 714 " (cutoff:3.500A) Proline residue: A 725 - end of helix Processing helix chain 'A' and resid 740 through 747 Processing sheet with id= A, first strand: chain 'A' and resid 167 through 170 removed outlier: 3.704A pdb=" N VAL A 69 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY A 107 " --> pdb=" O PRO A 138 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 885 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: 1.43 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 933 1.31 - 1.43: 1411 1.43 - 1.56: 3361 1.56 - 1.69: 0 1.69 - 1.81: 55 Bond restraints: 5760 Sorted by residual: bond pdb=" C31 1I2 A1101 " pdb=" C37 1I2 A1101 " ideal model delta sigma weight residual 0.000 1.542 -1.542 2.00e-02 2.50e+03 5.94e+03 bond pdb=" C33 1I2 A1101 " pdb=" C34 1I2 A1101 " ideal model delta sigma weight residual 0.359 1.540 -1.181 2.00e-02 2.50e+03 3.49e+03 bond pdb=" C29 1I2 A1101 " pdb=" C36 1I2 A1101 " ideal model delta sigma weight residual 0.947 1.545 -0.598 2.00e-02 2.50e+03 8.94e+02 bond pdb=" C35 1I2 A1101 " pdb=" C36 1I2 A1101 " ideal model delta sigma weight residual 0.948 1.531 -0.583 2.00e-02 2.50e+03 8.50e+02 bond pdb=" C28 1I2 A1101 " pdb=" N27 1I2 A1101 " ideal model delta sigma weight residual 1.945 1.450 0.495 2.00e-02 2.50e+03 6.13e+02 ... (remaining 5755 not shown) Histogram of bond angle deviations from ideal: 99.92 - 106.94: 200 106.94 - 113.95: 3382 113.95 - 120.97: 2754 120.97 - 127.98: 1449 127.98 - 134.99: 57 Bond angle restraints: 7842 Sorted by residual: angle pdb=" C29 1I2 A1101 " pdb=" C36 1I2 A1101 " pdb=" C35 1I2 A1101 " ideal model delta sigma weight residual 80.06 110.22 -30.16 3.00e+00 1.11e-01 1.01e+02 angle pdb=" C31 1I2 A1101 " pdb=" C37 1I2 A1101 " pdb=" C35 1I2 A1101 " ideal model delta sigma weight residual 81.83 110.67 -28.84 3.00e+00 1.11e-01 9.24e+01 angle pdb=" C32 1I2 A1101 " pdb=" C31 1I2 A1101 " pdb=" C37 1I2 A1101 " ideal model delta sigma weight residual 87.31 106.25 -18.94 3.00e+00 1.11e-01 3.99e+01 angle pdb=" C28 1I2 A1101 " pdb=" C31 1I2 A1101 " pdb=" C37 1I2 A1101 " ideal model delta sigma weight residual 87.11 105.91 -18.80 3.00e+00 1.11e-01 3.93e+01 angle pdb=" C31 1I2 A1101 " pdb=" C28 1I2 A1101 " pdb=" N27 1I2 A1101 " ideal model delta sigma weight residual 92.24 109.09 -16.85 3.00e+00 1.11e-01 3.16e+01 ... (remaining 7837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 3030 17.00 - 34.00: 316 34.00 - 51.00: 66 51.00 - 68.00: 11 68.00 - 85.00: 7 Dihedral angle restraints: 3430 sinusoidal: 1341 harmonic: 2089 Sorted by residual: dihedral pdb=" CA THR A 82 " pdb=" C THR A 82 " pdb=" N ASP A 83 " pdb=" CA ASP A 83 " ideal model delta harmonic sigma weight residual 180.00 162.28 17.72 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ARG A 720 " pdb=" C ARG A 720 " pdb=" N MET A 721 " pdb=" CA MET A 721 " ideal model delta harmonic sigma weight residual -180.00 -162.53 -17.47 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ASP A 83 " pdb=" CB ASP A 83 " pdb=" CG ASP A 83 " pdb=" OD1 ASP A 83 " ideal model delta sinusoidal sigma weight residual -30.00 -88.43 58.43 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 3427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.951: 928 0.951 - 1.902: 1 1.902 - 2.853: 1 2.853 - 3.804: 0 3.804 - 4.756: 1 Chirality restraints: 931 Sorted by residual: chirality pdb=" C35 1I2 A1101 " pdb=" C34 1I2 A1101 " pdb=" C36 1I2 A1101 " pdb=" C37 1I2 A1101 " both_signs ideal model delta sigma weight residual False -1.87 2.89 -4.76 2.00e-01 2.50e+01 5.65e+02 chirality pdb=" C33 1I2 A1101 " pdb=" C30 1I2 A1101 " pdb=" C32 1I2 A1101 " pdb=" C34 1I2 A1101 " both_signs ideal model delta sigma weight residual False -0.77 -2.74 1.97 2.00e-01 2.50e+01 9.71e+01 chirality pdb=" C28 1I2 A1101 " pdb=" C29 1I2 A1101 " pdb=" C31 1I2 A1101 " pdb=" N27 1I2 A1101 " both_signs ideal model delta sigma weight residual False -3.66 -2.40 -1.27 2.00e-01 2.50e+01 4.01e+01 ... (remaining 928 not shown) Planarity restraints: 990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 720 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.73e+00 pdb=" C ARG A 720 " 0.041 2.00e-02 2.50e+03 pdb=" O ARG A 720 " -0.015 2.00e-02 2.50e+03 pdb=" N MET A 721 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 736 " -0.011 2.00e-02 2.50e+03 2.32e-02 5.38e+00 pdb=" C TRP A 736 " 0.040 2.00e-02 2.50e+03 pdb=" O TRP A 736 " -0.016 2.00e-02 2.50e+03 pdb=" N TRP A 737 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 716 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" C ALA A 716 " 0.038 2.00e-02 2.50e+03 pdb=" O ALA A 716 " -0.014 2.00e-02 2.50e+03 pdb=" N THR A 717 " -0.013 2.00e-02 2.50e+03 ... (remaining 987 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 696 2.75 - 3.29: 6023 3.29 - 3.82: 9149 3.82 - 4.36: 9959 4.36 - 4.90: 17776 Nonbonded interactions: 43603 Sorted by model distance: nonbonded pdb=" O GLN A 140 " pdb=" ND2 ASN A 150 " model vdw 2.209 2.520 nonbonded pdb=" OE1 GLN A 49 " pdb=" NH1 ARG A 534 " model vdw 2.215 2.520 nonbonded pdb=" O GLN A 87 " pdb=" OG1 THR A 91 " model vdw 2.262 2.440 nonbonded pdb=" NH2 ARG A 65 " pdb=" O GLY A 141 " model vdw 2.272 2.520 nonbonded pdb=" NH1 ARG A 230 " pdb=" OE2 GLU A 234 " model vdw 2.282 2.520 ... (remaining 43598 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 3.890 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 18.970 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 : 0.033 1.542 5760 Z= 2.208 Angle : 0.942 30.155 7842 Z= 0.430 Chirality : 0.180 4.756 931 Planarity : 0.005 0.040 990 Dihedral : 14.669 85.001 2086 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.22 % Favored : 91.51 % Rotamer: Outliers : 0.50 % Allowed : 7.01 % Favored : 92.49 % 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: -2.32 (0.29), residues: 730 helix: -0.72 (0.22), residues: 465 sheet: -3.34 (0.63), residues: 41 loop : -2.71 (0.43), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 736 HIS 0.001 0.000 HIS A 132 PHE 0.015 0.001 PHE A 12 TYR 0.013 0.001 TYR A 10 ARG 0.002 0.000 ARG A 288 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 120 time to evaluate : 0.582 Fit side-chains REVERT: A 13 ARG cc_start: 0.7708 (pmt170) cc_final: 0.7409 (ptp90) REVERT: A 284 MET cc_start: 0.6768 (mtp) cc_final: 0.6482 (mtp) REVERT: A 444 GLN cc_start: 0.8687 (tp40) cc_final: 0.8472 (tt0) REVERT: A 620 MET cc_start: 0.8322 (mmm) cc_final: 0.8085 (mmm) REVERT: A 662 MET cc_start: 0.7842 (mpp) cc_final: 0.7520 (mpp) REVERT: A 669 ARG cc_start: 0.8787 (ttp80) cc_final: 0.8279 (ttm110) REVERT: A 736 TRP cc_start: 0.8328 (OUTLIER) cc_final: 0.7345 (m100) outliers start: 3 outliers final: 1 residues processed: 122 average time/residue: 0.1750 time to fit residues: 27.8064 Evaluate side-chains 89 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 736 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.0711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 5760 Z= 0.319 Angle : 0.793 16.496 7842 Z= 0.371 Chirality : 0.092 2.468 931 Planarity : 0.006 0.058 990 Dihedral : 5.947 46.459 796 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.00 % Allowed : 13.86 % Favored : 84.14 % 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: -1.84 (0.30), residues: 730 helix: -0.23 (0.23), residues: 467 sheet: -3.22 (0.65), residues: 41 loop : -2.84 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 736 HIS 0.001 0.000 HIS A 132 PHE 0.016 0.002 PHE A 12 TYR 0.013 0.002 TYR A 10 ARG 0.005 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 0.692 Fit side-chains REVERT: A 13 ARG cc_start: 0.7696 (pmt170) cc_final: 0.7215 (ptp90) REVERT: A 284 MET cc_start: 0.6776 (mtp) cc_final: 0.6486 (mtp) REVERT: A 444 GLN cc_start: 0.8685 (tp40) cc_final: 0.8477 (tt0) REVERT: A 620 MET cc_start: 0.8305 (mmm) cc_final: 0.8096 (mmm) REVERT: A 662 MET cc_start: 0.7861 (mpp) cc_final: 0.7627 (mpp) REVERT: A 669 ARG cc_start: 0.8794 (ttp80) cc_final: 0.8212 (ttp-110) REVERT: A 736 TRP cc_start: 0.8326 (OUTLIER) cc_final: 0.7579 (m100) outliers start: 12 outliers final: 8 residues processed: 97 average time/residue: 0.1697 time to fit residues: 21.8077 Evaluate side-chains 96 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 736 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.0728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 5760 Z= 0.319 Angle : 0.792 16.496 7842 Z= 0.371 Chirality : 0.092 2.468 931 Planarity : 0.007 0.103 990 Dihedral : 5.948 46.521 796 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.50 % Allowed : 14.86 % Favored : 83.64 % 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: -1.84 (0.30), residues: 730 helix: -0.23 (0.23), residues: 467 sheet: -3.22 (0.65), residues: 41 loop : -2.84 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 736 HIS 0.001 0.000 HIS A 132 PHE 0.016 0.002 PHE A 12 TYR 0.013 0.002 TYR A 10 ARG 0.005 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 0.587 Fit side-chains REVERT: A 13 ARG cc_start: 0.7695 (pmt170) cc_final: 0.7214 (ptp90) REVERT: A 284 MET cc_start: 0.6777 (mtp) cc_final: 0.6487 (mtp) REVERT: A 444 GLN cc_start: 0.8684 (tp40) cc_final: 0.8477 (tt0) REVERT: A 620 MET cc_start: 0.8305 (mmm) cc_final: 0.8097 (mmm) REVERT: A 662 MET cc_start: 0.7851 (mpp) cc_final: 0.7627 (mpp) REVERT: A 669 ARG cc_start: 0.8779 (ttp80) cc_final: 0.8212 (ttp-110) REVERT: A 736 TRP cc_start: 0.8325 (OUTLIER) cc_final: 0.7579 (m100) outliers start: 9 outliers final: 8 residues processed: 90 average time/residue: 0.1944 time to fit residues: 22.7812 Evaluate side-chains 95 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 736 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 7 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.0725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 5760 Z= 0.319 Angle : 0.792 16.496 7842 Z= 0.371 Chirality : 0.092 2.468 931 Planarity : 0.007 0.103 990 Dihedral : 5.947 46.468 796 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.50 % Allowed : 14.86 % Favored : 83.64 % 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: -1.84 (0.30), residues: 730 helix: -0.23 (0.23), residues: 467 sheet: -3.22 (0.65), residues: 41 loop : -2.84 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 736 HIS 0.001 0.000 HIS A 132 PHE 0.016 0.002 PHE A 12 TYR 0.013 0.002 TYR A 10 ARG 0.005 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.669 Fit side-chains REVERT: A 13 ARG cc_start: 0.7694 (pmt170) cc_final: 0.7214 (ptp90) REVERT: A 284 MET cc_start: 0.6778 (mtp) cc_final: 0.6487 (mtp) REVERT: A 444 GLN cc_start: 0.8684 (tp40) cc_final: 0.8477 (tt0) REVERT: A 620 MET cc_start: 0.8306 (mmm) cc_final: 0.8097 (mmm) REVERT: A 662 MET cc_start: 0.7851 (mpp) cc_final: 0.7628 (mpp) REVERT: A 669 ARG cc_start: 0.8779 (ttp80) cc_final: 0.8212 (ttp-110) REVERT: A 736 TRP cc_start: 0.8325 (OUTLIER) cc_final: 0.7579 (m100) outliers start: 9 outliers final: 8 residues processed: 89 average time/residue: 0.1836 time to fit residues: 21.3858 Evaluate side-chains 94 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 736 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 5760 Z= 0.319 Angle : 0.792 16.496 7842 Z= 0.371 Chirality : 0.092 2.468 931 Planarity : 0.007 0.103 990 Dihedral : 5.947 46.469 796 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.50 % Allowed : 14.86 % Favored : 83.64 % 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: -1.84 (0.30), residues: 730 helix: -0.23 (0.23), residues: 467 sheet: -3.22 (0.65), residues: 41 loop : -2.84 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 736 HIS 0.001 0.000 HIS A 132 PHE 0.016 0.002 PHE A 12 TYR 0.013 0.002 TYR A 10 ARG 0.005 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.743 Fit side-chains REVERT: A 13 ARG cc_start: 0.7694 (pmt170) cc_final: 0.7214 (ptp90) REVERT: A 284 MET cc_start: 0.6778 (mtp) cc_final: 0.6487 (mtp) REVERT: A 444 GLN cc_start: 0.8683 (tp40) cc_final: 0.8477 (tt0) REVERT: A 620 MET cc_start: 0.8307 (mmm) cc_final: 0.8097 (mmm) REVERT: A 662 MET cc_start: 0.7851 (mpp) cc_final: 0.7628 (mpp) REVERT: A 669 ARG cc_start: 0.8779 (ttp80) cc_final: 0.8212 (ttp-110) REVERT: A 736 TRP cc_start: 0.8325 (OUTLIER) cc_final: 0.7579 (m100) outliers start: 9 outliers final: 8 residues processed: 88 average time/residue: 0.1753 time to fit residues: 20.3828 Evaluate side-chains 94 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 736 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 5760 Z= 0.319 Angle : 0.792 16.496 7842 Z= 0.371 Chirality : 0.092 2.468 931 Planarity : 0.007 0.103 990 Dihedral : 5.947 46.469 796 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.50 % Allowed : 14.86 % Favored : 83.64 % 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: -1.84 (0.30), residues: 730 helix: -0.23 (0.23), residues: 467 sheet: -3.22 (0.65), residues: 41 loop : -2.84 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 736 HIS 0.001 0.000 HIS A 132 PHE 0.016 0.002 PHE A 12 TYR 0.013 0.002 TYR A 10 ARG 0.005 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.626 Fit side-chains REVERT: A 13 ARG cc_start: 0.7694 (pmt170) cc_final: 0.7214 (ptp90) REVERT: A 284 MET cc_start: 0.6778 (mtp) cc_final: 0.6487 (mtp) REVERT: A 444 GLN cc_start: 0.8683 (tp40) cc_final: 0.8477 (tt0) REVERT: A 620 MET cc_start: 0.8307 (mmm) cc_final: 0.8097 (mmm) REVERT: A 662 MET cc_start: 0.7851 (mpp) cc_final: 0.7628 (mpp) REVERT: A 669 ARG cc_start: 0.8779 (ttp80) cc_final: 0.8212 (ttp-110) REVERT: A 736 TRP cc_start: 0.8325 (OUTLIER) cc_final: 0.7579 (m100) outliers start: 9 outliers final: 8 residues processed: 88 average time/residue: 0.1747 time to fit residues: 20.2100 Evaluate side-chains 94 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 736 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 7 optimal weight: 0.8980 chunk 40 optimal weight: 0.4980 chunk 51 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 5760 Z= 0.319 Angle : 0.792 16.496 7842 Z= 0.371 Chirality : 0.092 2.468 931 Planarity : 0.007 0.103 990 Dihedral : 5.947 46.469 796 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.50 % Allowed : 14.86 % Favored : 83.64 % 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: -1.84 (0.30), residues: 730 helix: -0.23 (0.23), residues: 467 sheet: -3.22 (0.65), residues: 41 loop : -2.84 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 736 HIS 0.001 0.000 HIS A 132 PHE 0.016 0.002 PHE A 12 TYR 0.013 0.002 TYR A 10 ARG 0.005 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.661 Fit side-chains REVERT: A 13 ARG cc_start: 0.7694 (pmt170) cc_final: 0.7214 (ptp90) REVERT: A 284 MET cc_start: 0.6778 (mtp) cc_final: 0.6487 (mtp) REVERT: A 444 GLN cc_start: 0.8683 (tp40) cc_final: 0.8477 (tt0) REVERT: A 620 MET cc_start: 0.8307 (mmm) cc_final: 0.8097 (mmm) REVERT: A 662 MET cc_start: 0.7851 (mpp) cc_final: 0.7628 (mpp) REVERT: A 669 ARG cc_start: 0.8779 (ttp80) cc_final: 0.8212 (ttp-110) REVERT: A 736 TRP cc_start: 0.8325 (OUTLIER) cc_final: 0.7579 (m100) outliers start: 9 outliers final: 8 residues processed: 88 average time/residue: 0.1838 time to fit residues: 21.3134 Evaluate side-chains 94 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 736 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 55 optimal weight: 0.2980 chunk 64 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 5760 Z= 0.319 Angle : 0.792 16.496 7842 Z= 0.371 Chirality : 0.092 2.468 931 Planarity : 0.007 0.103 990 Dihedral : 5.947 46.469 796 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.50 % Allowed : 14.86 % Favored : 83.64 % 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: -1.84 (0.30), residues: 730 helix: -0.23 (0.23), residues: 467 sheet: -3.22 (0.65), residues: 41 loop : -2.84 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 736 HIS 0.001 0.000 HIS A 132 PHE 0.016 0.002 PHE A 12 TYR 0.013 0.002 TYR A 10 ARG 0.005 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.750 Fit side-chains REVERT: A 13 ARG cc_start: 0.7694 (pmt170) cc_final: 0.7214 (ptp90) REVERT: A 284 MET cc_start: 0.6778 (mtp) cc_final: 0.6487 (mtp) REVERT: A 444 GLN cc_start: 0.8683 (tp40) cc_final: 0.8477 (tt0) REVERT: A 620 MET cc_start: 0.8307 (mmm) cc_final: 0.8097 (mmm) REVERT: A 662 MET cc_start: 0.7851 (mpp) cc_final: 0.7628 (mpp) REVERT: A 669 ARG cc_start: 0.8779 (ttp80) cc_final: 0.8212 (ttp-110) REVERT: A 736 TRP cc_start: 0.8325 (OUTLIER) cc_final: 0.7579 (m100) outliers start: 9 outliers final: 8 residues processed: 88 average time/residue: 0.1849 time to fit residues: 21.4767 Evaluate side-chains 94 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 736 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 59 optimal weight: 0.1980 chunk 62 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 69 optimal weight: 0.3980 chunk 42 optimal weight: 9.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 5760 Z= 0.319 Angle : 0.792 16.496 7842 Z= 0.371 Chirality : 0.092 2.468 931 Planarity : 0.007 0.103 990 Dihedral : 5.947 46.469 796 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.50 % Allowed : 14.86 % Favored : 83.64 % 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: -1.84 (0.30), residues: 730 helix: -0.23 (0.23), residues: 467 sheet: -3.22 (0.65), residues: 41 loop : -2.84 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 736 HIS 0.001 0.000 HIS A 132 PHE 0.016 0.002 PHE A 12 TYR 0.013 0.002 TYR A 10 ARG 0.005 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.635 Fit side-chains REVERT: A 13 ARG cc_start: 0.7694 (pmt170) cc_final: 0.7214 (ptp90) REVERT: A 284 MET cc_start: 0.6778 (mtp) cc_final: 0.6487 (mtp) REVERT: A 444 GLN cc_start: 0.8683 (tp40) cc_final: 0.8477 (tt0) REVERT: A 620 MET cc_start: 0.8307 (mmm) cc_final: 0.8097 (mmm) REVERT: A 662 MET cc_start: 0.7851 (mpp) cc_final: 0.7628 (mpp) REVERT: A 669 ARG cc_start: 0.8779 (ttp80) cc_final: 0.8212 (ttp-110) REVERT: A 736 TRP cc_start: 0.8325 (OUTLIER) cc_final: 0.7579 (m100) outliers start: 9 outliers final: 8 residues processed: 88 average time/residue: 0.1830 time to fit residues: 21.2124 Evaluate side-chains 94 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 736 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 66 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 5760 Z= 0.319 Angle : 0.792 16.496 7842 Z= 0.371 Chirality : 0.092 2.468 931 Planarity : 0.007 0.103 990 Dihedral : 5.947 46.469 796 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.50 % Allowed : 14.86 % Favored : 83.64 % 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: -1.84 (0.30), residues: 730 helix: -0.23 (0.23), residues: 467 sheet: -3.22 (0.65), residues: 41 loop : -2.84 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 736 HIS 0.001 0.000 HIS A 132 PHE 0.016 0.002 PHE A 12 TYR 0.013 0.002 TYR A 10 ARG 0.005 0.000 ARG A 514 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.689 Fit side-chains REVERT: A 13 ARG cc_start: 0.7694 (pmt170) cc_final: 0.7214 (ptp90) REVERT: A 284 MET cc_start: 0.6778 (mtp) cc_final: 0.6487 (mtp) REVERT: A 444 GLN cc_start: 0.8683 (tp40) cc_final: 0.8477 (tt0) REVERT: A 620 MET cc_start: 0.8307 (mmm) cc_final: 0.8097 (mmm) REVERT: A 662 MET cc_start: 0.7851 (mpp) cc_final: 0.7628 (mpp) REVERT: A 669 ARG cc_start: 0.8779 (ttp80) cc_final: 0.8212 (ttp-110) REVERT: A 736 TRP cc_start: 0.8325 (OUTLIER) cc_final: 0.7579 (m100) outliers start: 9 outliers final: 8 residues processed: 88 average time/residue: 0.1731 time to fit residues: 20.1707 Evaluate side-chains 94 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 736 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 41 optimal weight: 0.0470 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.127769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.091600 restraints weight = 12077.443| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.52 r_work: 0.3020 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 5760 Z= 0.319 Angle : 0.792 16.496 7842 Z= 0.371 Chirality : 0.092 2.468 931 Planarity : 0.007 0.103 990 Dihedral : 5.947 46.469 796 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.50 % Allowed : 14.86 % Favored : 83.64 % 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: -1.84 (0.30), residues: 730 helix: -0.23 (0.23), residues: 467 sheet: -3.22 (0.65), residues: 41 loop : -2.84 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 736 HIS 0.001 0.000 HIS A 132 PHE 0.016 0.002 PHE A 12 TYR 0.013 0.002 TYR A 10 ARG 0.005 0.000 ARG A 514 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1398.54 seconds wall clock time: 25 minutes 44.21 seconds (1544.21 seconds total)