Starting phenix.real_space_refine on Thu Feb 15 04:00:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrg_14913/02_2024/7zrg_14913_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrg_14913/02_2024/7zrg_14913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrg_14913/02_2024/7zrg_14913.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrg_14913/02_2024/7zrg_14913.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrg_14913/02_2024/7zrg_14913_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrg_14913/02_2024/7zrg_14913_updated.pdb" } resolution = 3.5 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 7 8.98 5 P 8 5.49 5 S 62 5.16 5 C 7124 2.51 5 N 1824 2.21 5 O 2007 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 45": "OE1" <-> "OE2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B GLU 296": "OE1" <-> "OE2" Residue "B GLU 330": "OE1" <-> "OE2" Residue "B GLU 560": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11032 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4155 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "C" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1431 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 13, 'TRANS': 176} Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 200 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "B" Number of atoms: 5008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5008 Classifications: {'peptide': 674} Link IDs: {'PTRANS': 26, 'TRANS': 647} Chain: "A" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 207 Unusual residues: {' K': 7, 'CDL': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.41, per 1000 atoms: 0.58 Number of scatterers: 11032 At special positions: 0 Unit cell: (100.188, 111.32, 148.764, 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) K 7 19.00 S 62 16.00 P 8 15.00 O 2007 8.00 N 1824 7.00 C 7124 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: 4.38 Conformation dependent library (CDL) restraints added in 2.3 seconds 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2634 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 6 sheets defined 55.7% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'A' and resid 2 through 31 removed outlier: 3.959A pdb=" N MET A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 40 through 50 Processing helix chain 'A' and resid 59 through 82 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 126 through 156 removed outlier: 4.183A pdb=" N LEU A 133 " --> pdb=" O GLN A 129 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR A 134 " --> pdb=" O MET A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 178 through 192 Processing helix chain 'A' and resid 219 through 228 removed outlier: 3.794A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 273 removed outlier: 4.388A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 277 through 304 Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 329 through 341 Processing helix chain 'A' and resid 356 through 367 removed outlier: 3.748A pdb=" N VAL A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 378 through 398 Processing helix chain 'A' and resid 411 through 435 removed outlier: 4.562A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 449 through 464 Processing helix chain 'A' and resid 479 through 494 Processing helix chain 'A' and resid 497 through 508 Processing helix chain 'A' and resid 524 through 541 Processing helix chain 'A' and resid 544 through 549 Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'C' and resid 4 through 20 Processing helix chain 'C' and resid 22 through 33 Processing helix chain 'C' and resid 35 through 38 No H-bonds generated for 'chain 'C' and resid 35 through 38' Processing helix chain 'C' and resid 92 through 108 Processing helix chain 'C' and resid 118 through 121 No H-bonds generated for 'chain 'C' and resid 118 through 121' Processing helix chain 'C' and resid 134 through 148 Proline residue: C 142 - end of helix Processing helix chain 'C' and resid 152 through 161 Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'D' and resid 3 through 24 Processing helix chain 'B' and resid 12 through 23 removed outlier: 4.748A pdb=" N ALA B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU B 20 " --> pdb=" O GLN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 53 Processing helix chain 'B' and resid 62 through 96 removed outlier: 3.666A pdb=" N VAL B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 208 Processing helix chain 'B' and resid 216 through 245 removed outlier: 3.878A pdb=" N LEU B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TRP B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix removed outlier: 4.162A pdb=" N TRP B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 262 Processing helix chain 'B' and resid 265 through 285 removed outlier: 5.434A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 298 Processing helix chain 'B' and resid 330 through 340 Processing helix chain 'B' and resid 347 through 359 Processing helix chain 'B' and resid 398 through 405 Processing helix chain 'B' and resid 414 through 426 Processing helix chain 'B' and resid 454 through 463 removed outlier: 3.715A pdb=" N LYS B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N MET B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 496 through 509 removed outlier: 3.658A pdb=" N GLU B 509 " --> pdb=" O GLN B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 527 Proline residue: B 524 - end of helix Processing helix chain 'B' and resid 540 through 543 No H-bonds generated for 'chain 'B' and resid 540 through 543' Processing helix chain 'B' and resid 558 through 594 removed outlier: 4.123A pdb=" N ASP B 583 " --> pdb=" O SER B 579 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL B 584 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA B 585 " --> pdb=" O ALA B 581 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 600 through 605 removed outlier: 3.751A pdb=" N ASN B 603 " --> pdb=" O PRO B 600 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 630 removed outlier: 4.488A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 637 Processing helix chain 'B' and resid 646 through 679 removed outlier: 4.044A pdb=" N GLY B 658 " --> pdb=" O LEU B 654 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLY B 661 " --> pdb=" O TYR B 657 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU B 662 " --> pdb=" O GLY B 658 " (cutoff:3.500A) Proline residue: B 665 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 202 through 204 Processing sheet with id= B, first strand: chain 'C' and resid 42 through 44 removed outlier: 3.599A pdb=" N GLY C 51 " --> pdb=" O ILE C 43 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 131 through 134 removed outlier: 3.645A pdb=" N GLU B 145 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 287 through 289 Processing sheet with id= E, first strand: chain 'B' and resid 429 through 431 Processing sheet with id= F, first strand: chain 'B' and resid 514 through 516 removed outlier: 6.939A pdb=" N VAL B 531 " --> pdb=" O MET B 515 " (cutoff:3.500A) No H-bonds generated for sheet with id= F 555 hydrogen bonds defined for protein. 1602 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: 2.92 Time building geometry restraints manager: 4.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1946 1.33 - 1.45: 2647 1.45 - 1.57: 6503 1.57 - 1.70: 17 1.70 - 1.82: 112 Bond restraints: 11225 Sorted by residual: bond pdb=" OA3 CDL A 609 " pdb=" PA1 CDL A 609 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.44e+00 bond pdb=" OA3 CDL A 608 " pdb=" PA1 CDL A 608 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.11e+00 bond pdb=" OB3 CDL A 608 " pdb=" PB2 CDL A 608 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.08e+00 bond pdb=" OB3 CDL A 609 " pdb=" PB2 CDL A 609 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.08e+00 bond pdb=" C11 CDL A 608 " pdb=" C12 CDL A 608 " ideal model delta sigma weight residual 1.523 1.491 0.032 1.50e-02 4.44e+03 4.48e+00 ... (remaining 11220 not shown) Histogram of bond angle deviations from ideal: 99.13 - 107.28: 407 107.28 - 115.42: 6963 115.42 - 123.57: 7557 123.57 - 131.72: 279 131.72 - 139.86: 32 Bond angle restraints: 15238 Sorted by residual: angle pdb=" CA TYR A 381 " pdb=" CB TYR A 381 " pdb=" CG TYR A 381 " ideal model delta sigma weight residual 113.90 120.97 -7.07 1.80e+00 3.09e-01 1.54e+01 angle pdb=" C ASP B 366 " pdb=" N VAL B 367 " pdb=" CA VAL B 367 " ideal model delta sigma weight residual 121.97 128.98 -7.01 1.80e+00 3.09e-01 1.52e+01 angle pdb=" CB MET B 36 " pdb=" CG MET B 36 " pdb=" SD MET B 36 " ideal model delta sigma weight residual 112.70 123.29 -10.59 3.00e+00 1.11e-01 1.25e+01 angle pdb=" CB MET A 274 " pdb=" CG MET A 274 " pdb=" SD MET A 274 " ideal model delta sigma weight residual 112.70 123.10 -10.40 3.00e+00 1.11e-01 1.20e+01 angle pdb=" C LEU A 178 " pdb=" N VAL A 179 " pdb=" CA VAL A 179 " ideal model delta sigma weight residual 120.33 123.10 -2.77 8.00e-01 1.56e+00 1.20e+01 ... (remaining 15233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.78: 5978 18.78 - 37.56: 589 37.56 - 56.34: 142 56.34 - 75.12: 38 75.12 - 93.90: 14 Dihedral angle restraints: 6761 sinusoidal: 2661 harmonic: 4100 Sorted by residual: dihedral pdb=" CA ALA A 470 " pdb=" C ALA A 470 " pdb=" N PHE A 471 " pdb=" CA PHE A 471 " ideal model delta harmonic sigma weight residual 180.00 161.07 18.93 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA GLY B 658 " pdb=" C GLY B 658 " pdb=" N LEU B 659 " pdb=" CA LEU B 659 " ideal model delta harmonic sigma weight residual 180.00 161.67 18.33 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA5 CDL A 608 " pdb=" CA4 CDL A 608 " pdb=" OA6 CDL A 608 " pdb=" CA6 CDL A 608 " ideal model delta sinusoidal sigma weight residual 168.24 -97.86 -93.90 1 3.00e+01 1.11e-03 1.14e+01 ... (remaining 6758 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1405 0.052 - 0.103: 337 0.103 - 0.155: 60 0.155 - 0.206: 5 0.206 - 0.258: 5 Chirality restraints: 1812 Sorted by residual: chirality pdb=" CA4 CDL A 608 " pdb=" CA3 CDL A 608 " pdb=" CA6 CDL A 608 " pdb=" OA6 CDL A 608 " both_signs ideal model delta sigma weight residual False -2.57 -2.32 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB VAL B 664 " pdb=" CA VAL B 664 " pdb=" CG1 VAL B 664 " pdb=" CG2 VAL B 664 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB ILE B 182 " pdb=" CA ILE B 182 " pdb=" CG1 ILE B 182 " pdb=" CG2 ILE B 182 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1809 not shown) Planarity restraints: 1908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 105 " -0.016 2.00e-02 2.50e+03 2.09e-02 7.67e+00 pdb=" CG PHE B 105 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE B 105 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B 105 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE B 105 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 105 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 105 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 381 " 0.017 2.00e-02 2.50e+03 1.43e-02 4.08e+00 pdb=" CG TYR A 381 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A 381 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 381 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 381 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 381 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 381 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 381 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 361 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.90e+00 pdb=" N PRO A 362 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 362 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 362 " 0.028 5.00e-02 4.00e+02 ... (remaining 1905 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.86: 3802 2.86 - 3.43: 12578 3.43 - 4.00: 21527 4.00 - 4.57: 30664 4.57 - 5.14: 43138 Nonbonded interactions: 111709 Sorted by model distance: nonbonded pdb=" O LEU A 541 " pdb=" OH TYR B 587 " model vdw 2.291 2.440 nonbonded pdb=" OG SER A 325 " pdb=" O ASN C 131 " model vdw 2.295 2.440 nonbonded pdb=" O SER A 119 " pdb=" OG1 THR A 123 " model vdw 2.300 2.440 nonbonded pdb=" OD1 ASN B 474 " pdb=" OG1 THR B 477 " model vdw 2.301 2.440 nonbonded pdb=" OG SER A 343 " pdb=" O ASN A 466 " model vdw 2.304 2.440 ... (remaining 111704 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.640 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 32.840 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11225 Z= 0.254 Angle : 0.782 10.595 15238 Z= 0.396 Chirality : 0.046 0.258 1812 Planarity : 0.005 0.049 1908 Dihedral : 16.908 93.902 4127 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: -1.09 (0.21), residues: 1437 helix: 0.09 (0.16), residues: 881 sheet: -1.58 (0.57), residues: 87 loop : -2.02 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 176 HIS 0.003 0.001 HIS A 242 PHE 0.048 0.002 PHE B 105 TYR 0.035 0.002 TYR A 381 ARG 0.008 0.000 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.208 Fit side-chains revert: symmetry clash REVERT: A 126 TYR cc_start: 0.8029 (m-10) cc_final: 0.7828 (m-10) REVERT: B 515 MET cc_start: 0.7513 (ptm) cc_final: 0.7248 (ppp) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2258 time to fit residues: 53.4670 Evaluate side-chains 136 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.0000 chunk 108 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 129 optimal weight: 0.0040 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 GLN ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11225 Z= 0.220 Angle : 0.552 7.393 15238 Z= 0.274 Chirality : 0.039 0.162 1812 Planarity : 0.004 0.050 1908 Dihedral : 12.672 86.681 1747 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.62 % Allowed : 8.20 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.22), residues: 1437 helix: 0.88 (0.17), residues: 877 sheet: -1.52 (0.63), residues: 72 loop : -1.86 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 31 HIS 0.003 0.001 HIS A 451 PHE 0.017 0.002 PHE B 105 TYR 0.024 0.002 TYR A 381 ARG 0.002 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 150 time to evaluate : 1.141 Fit side-chains REVERT: A 126 TYR cc_start: 0.8129 (m-10) cc_final: 0.7876 (m-10) REVERT: B 515 MET cc_start: 0.7520 (ptm) cc_final: 0.7318 (ppp) outliers start: 7 outliers final: 5 residues processed: 154 average time/residue: 0.2225 time to fit residues: 49.5993 Evaluate side-chains 144 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 139 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 598 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 88 optimal weight: 20.0000 chunk 35 optimal weight: 4.9990 chunk 130 optimal weight: 0.0270 chunk 140 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 129 optimal weight: 0.6980 chunk 44 optimal weight: 20.0000 chunk 104 optimal weight: 0.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11225 Z= 0.154 Angle : 0.508 8.722 15238 Z= 0.249 Chirality : 0.038 0.160 1812 Planarity : 0.003 0.045 1908 Dihedral : 11.837 84.571 1747 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.23 % Allowed : 10.85 % Favored : 87.92 % 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: 0.12 (0.22), residues: 1437 helix: 1.23 (0.18), residues: 867 sheet: -1.52 (0.64), residues: 73 loop : -1.74 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 71 HIS 0.002 0.000 HIS B 404 PHE 0.014 0.001 PHE B 105 TYR 0.024 0.001 TYR A 381 ARG 0.002 0.000 ARG B 394 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 146 time to evaluate : 1.185 Fit side-chains REVERT: A 489 MET cc_start: 0.8567 (mtm) cc_final: 0.8309 (mtt) REVERT: B 560 GLU cc_start: 0.7044 (pm20) cc_final: 0.6823 (mp0) outliers start: 14 outliers final: 9 residues processed: 151 average time/residue: 0.2135 time to fit residues: 47.4199 Evaluate side-chains 145 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 136 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 0.2980 chunk 97 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 130 optimal weight: 0.7980 chunk 138 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11225 Z= 0.256 Angle : 0.553 9.304 15238 Z= 0.273 Chirality : 0.040 0.189 1812 Planarity : 0.004 0.061 1908 Dihedral : 11.526 85.914 1747 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.68 % Allowed : 12.08 % Favored : 86.24 % 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: 0.06 (0.22), residues: 1437 helix: 1.16 (0.17), residues: 862 sheet: -1.50 (0.64), residues: 73 loop : -1.70 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 71 HIS 0.003 0.001 HIS A 451 PHE 0.015 0.001 PHE A 471 TYR 0.025 0.002 TYR A 381 ARG 0.002 0.000 ARG B 359 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 1.221 Fit side-chains revert: symmetry clash REVERT: A 327 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8486 (m-80) REVERT: A 436 MET cc_start: 0.8784 (mmm) cc_final: 0.8516 (mmp) REVERT: C 22 TYR cc_start: 0.8639 (t80) cc_final: 0.8389 (t80) REVERT: B 125 GLN cc_start: 0.5388 (pm20) cc_final: 0.5094 (tm-30) REVERT: B 213 ARG cc_start: 0.7483 (tpm170) cc_final: 0.7167 (tpm170) REVERT: B 560 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6804 (mp0) outliers start: 19 outliers final: 13 residues processed: 144 average time/residue: 0.2093 time to fit residues: 44.8360 Evaluate side-chains 144 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 124 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11225 Z= 0.165 Angle : 0.496 7.136 15238 Z= 0.246 Chirality : 0.038 0.146 1812 Planarity : 0.003 0.036 1908 Dihedral : 11.120 84.737 1747 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.59 % Allowed : 13.14 % Favored : 85.27 % 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: 0.27 (0.22), residues: 1437 helix: 1.34 (0.18), residues: 860 sheet: -1.55 (0.65), residues: 73 loop : -1.60 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 71 HIS 0.002 0.000 HIS B 404 PHE 0.013 0.001 PHE A 373 TYR 0.023 0.001 TYR A 381 ARG 0.001 0.000 ARG B 394 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 144 time to evaluate : 1.320 Fit side-chains REVERT: A 190 ILE cc_start: 0.9091 (mm) cc_final: 0.8631 (mt) REVERT: A 235 PHE cc_start: 0.8395 (t80) cc_final: 0.8132 (t80) REVERT: A 471 PHE cc_start: 0.7070 (OUTLIER) cc_final: 0.6008 (m-10) REVERT: C 22 TYR cc_start: 0.8618 (t80) cc_final: 0.8380 (t80) REVERT: B 13 LEU cc_start: 0.7828 (pt) cc_final: 0.6984 (tp) REVERT: B 125 GLN cc_start: 0.5557 (pm20) cc_final: 0.5114 (tm-30) REVERT: B 213 ARG cc_start: 0.7471 (tpm170) cc_final: 0.7200 (tpm170) REVERT: B 463 MET cc_start: 0.5409 (mtm) cc_final: 0.5200 (mtm) REVERT: B 560 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6814 (mp0) outliers start: 18 outliers final: 11 residues processed: 156 average time/residue: 0.2189 time to fit residues: 50.3063 Evaluate side-chains 145 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 132 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 1.9990 chunk 124 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 GLN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11225 Z= 0.197 Angle : 0.518 7.152 15238 Z= 0.257 Chirality : 0.038 0.149 1812 Planarity : 0.003 0.037 1908 Dihedral : 10.984 85.569 1747 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.68 % Allowed : 14.64 % Favored : 83.69 % 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: 0.27 (0.22), residues: 1437 helix: 1.33 (0.17), residues: 861 sheet: -1.54 (0.65), residues: 73 loop : -1.60 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 71 HIS 0.002 0.001 HIS B 404 PHE 0.013 0.001 PHE A 373 TYR 0.024 0.001 TYR A 381 ARG 0.002 0.000 ARG B 394 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 1.233 Fit side-chains REVERT: A 327 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8482 (m-80) REVERT: A 410 ASP cc_start: 0.7911 (p0) cc_final: 0.7696 (p0) REVERT: A 471 PHE cc_start: 0.7139 (OUTLIER) cc_final: 0.5946 (m-10) REVERT: C 22 TYR cc_start: 0.8601 (t80) cc_final: 0.8365 (t80) REVERT: B 13 LEU cc_start: 0.7809 (pt) cc_final: 0.7483 (pp) REVERT: B 125 GLN cc_start: 0.5501 (pm20) cc_final: 0.5074 (tm-30) REVERT: B 213 ARG cc_start: 0.7474 (tpm170) cc_final: 0.7224 (tpm170) outliers start: 19 outliers final: 13 residues processed: 151 average time/residue: 0.2174 time to fit residues: 48.0600 Evaluate side-chains 149 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 86 optimal weight: 40.0000 chunk 84 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11225 Z= 0.207 Angle : 0.523 7.509 15238 Z= 0.259 Chirality : 0.039 0.148 1812 Planarity : 0.003 0.039 1908 Dihedral : 10.904 88.341 1747 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.68 % Allowed : 15.08 % 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: 0.27 (0.22), residues: 1437 helix: 1.33 (0.17), residues: 857 sheet: -1.58 (0.65), residues: 73 loop : -1.57 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 71 HIS 0.002 0.001 HIS B 404 PHE 0.014 0.001 PHE A 373 TYR 0.024 0.001 TYR A 381 ARG 0.002 0.000 ARG B 394 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 139 time to evaluate : 1.252 Fit side-chains REVERT: A 327 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.8400 (m-80) REVERT: A 471 PHE cc_start: 0.7253 (OUTLIER) cc_final: 0.6033 (m-10) REVERT: B 13 LEU cc_start: 0.7785 (pt) cc_final: 0.7522 (pp) REVERT: B 125 GLN cc_start: 0.5486 (pm20) cc_final: 0.5025 (tm-30) REVERT: B 213 ARG cc_start: 0.7418 (tpm170) cc_final: 0.7193 (tpm170) REVERT: B 463 MET cc_start: 0.4528 (mtt) cc_final: 0.4136 (mtm) outliers start: 19 outliers final: 16 residues processed: 154 average time/residue: 0.2233 time to fit residues: 51.1637 Evaluate side-chains 153 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 0.0770 chunk 82 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 87 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11225 Z= 0.189 Angle : 0.518 7.915 15238 Z= 0.256 Chirality : 0.038 0.145 1812 Planarity : 0.003 0.037 1908 Dihedral : 10.681 88.453 1747 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.85 % Allowed : 14.81 % Favored : 83.33 % 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: 0.27 (0.22), residues: 1437 helix: 1.33 (0.17), residues: 862 sheet: -1.67 (0.62), residues: 78 loop : -1.59 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 71 HIS 0.003 0.001 HIS B 404 PHE 0.013 0.001 PHE A 373 TYR 0.024 0.001 TYR A 381 ARG 0.001 0.000 ARG B 394 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 1.320 Fit side-chains REVERT: A 327 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8377 (m-80) REVERT: A 471 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.6013 (m-10) REVERT: B 13 LEU cc_start: 0.7734 (pt) cc_final: 0.7492 (pp) REVERT: B 125 GLN cc_start: 0.5500 (pm20) cc_final: 0.5053 (tm-30) REVERT: B 213 ARG cc_start: 0.7447 (tpm170) cc_final: 0.7216 (tpm170) REVERT: B 448 ILE cc_start: 0.6963 (tp) cc_final: 0.6560 (tt) REVERT: B 463 MET cc_start: 0.4881 (mtt) cc_final: 0.4554 (mtm) outliers start: 21 outliers final: 17 residues processed: 154 average time/residue: 0.2223 time to fit residues: 50.8661 Evaluate side-chains 152 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 0.9990 chunk 120 optimal weight: 0.0070 chunk 128 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 121 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11225 Z= 0.159 Angle : 0.504 8.325 15238 Z= 0.248 Chirality : 0.038 0.141 1812 Planarity : 0.003 0.037 1908 Dihedral : 10.375 84.348 1747 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.50 % Allowed : 15.26 % 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: 0.37 (0.22), residues: 1437 helix: 1.47 (0.18), residues: 855 sheet: -1.63 (0.62), residues: 78 loop : -1.62 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 245 HIS 0.003 0.000 HIS B 404 PHE 0.012 0.001 PHE A 373 TYR 0.023 0.001 TYR A 381 ARG 0.001 0.000 ARG B 394 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 1.132 Fit side-chains REVERT: A 471 PHE cc_start: 0.6889 (OUTLIER) cc_final: 0.5842 (m-10) REVERT: B 13 LEU cc_start: 0.7698 (pt) cc_final: 0.7453 (pp) REVERT: B 125 GLN cc_start: 0.5638 (pm20) cc_final: 0.5147 (tm-30) REVERT: B 213 ARG cc_start: 0.7433 (tpm170) cc_final: 0.7210 (tpm170) REVERT: B 463 MET cc_start: 0.4766 (mtt) cc_final: 0.4412 (mtm) outliers start: 17 outliers final: 15 residues processed: 151 average time/residue: 0.2238 time to fit residues: 49.4988 Evaluate side-chains 147 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 94 optimal weight: 0.0270 chunk 142 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 87 optimal weight: 30.0000 chunk 69 optimal weight: 0.7980 chunk 90 optimal weight: 10.0000 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11225 Z= 0.165 Angle : 0.509 8.551 15238 Z= 0.250 Chirality : 0.038 0.142 1812 Planarity : 0.003 0.037 1908 Dihedral : 10.260 81.193 1747 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.59 % Allowed : 15.17 % 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: 0.40 (0.22), residues: 1437 helix: 1.51 (0.18), residues: 853 sheet: -1.63 (0.62), residues: 78 loop : -1.62 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 71 HIS 0.003 0.000 HIS B 404 PHE 0.012 0.001 PHE A 373 TYR 0.023 0.001 TYR A 381 ARG 0.001 0.000 ARG A 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 1.272 Fit side-chains REVERT: A 471 PHE cc_start: 0.6904 (OUTLIER) cc_final: 0.5864 (m-10) REVERT: B 13 LEU cc_start: 0.7695 (pt) cc_final: 0.7456 (pp) REVERT: B 125 GLN cc_start: 0.5624 (pm20) cc_final: 0.5096 (tm-30) REVERT: B 213 ARG cc_start: 0.7451 (tpm170) cc_final: 0.7229 (tpm170) REVERT: B 463 MET cc_start: 0.4762 (mtt) cc_final: 0.4548 (mtm) outliers start: 18 outliers final: 15 residues processed: 147 average time/residue: 0.2138 time to fit residues: 46.8709 Evaluate side-chains 146 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.8980 chunk 34 optimal weight: 0.4980 chunk 104 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 113 optimal weight: 20.0000 chunk 47 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** 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 = 0.3664 r_free = 0.3664 target = 0.140641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.102400 restraints weight = 15146.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.101272 restraints weight = 12695.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.101917 restraints weight = 11754.120| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11225 Z= 0.179 Angle : 0.513 8.560 15238 Z= 0.252 Chirality : 0.038 0.144 1812 Planarity : 0.003 0.037 1908 Dihedral : 10.181 79.489 1747 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.94 % Allowed : 14.73 % Favored : 83.33 % 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: 0.37 (0.22), residues: 1437 helix: 1.44 (0.17), residues: 859 sheet: -1.61 (0.62), residues: 78 loop : -1.57 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 71 HIS 0.003 0.001 HIS B 404 PHE 0.013 0.001 PHE A 373 TYR 0.024 0.001 TYR A 381 ARG 0.001 0.000 ARG A 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2049.51 seconds wall clock time: 38 minutes 22.10 seconds (2302.10 seconds total)