Starting phenix.real_space_refine on Wed Nov 15 07:55:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrg_14913/11_2023/7zrg_14913_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrg_14913/11_2023/7zrg_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_14913/11_2023/7zrg_14913.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrg_14913/11_2023/7zrg_14913.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrg_14913/11_2023/7zrg_14913_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrg_14913/11_2023/7zrg_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 6.43, 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: 4.98 Conformation dependent library (CDL) restraints added in 2.4 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: 2.32 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: 3.12 Time building geometry restraints manager: 5.02 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 - 17.62: 5892 17.62 - 35.24: 597 35.24 - 52.86: 148 52.86 - 70.48: 37 70.48 - 88.10: 16 Dihedral angle restraints: 6690 sinusoidal: 2590 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=" CA ASP B 119 " pdb=" CB ASP B 119 " pdb=" CG ASP B 119 " pdb=" OD1 ASP B 119 " ideal model delta sinusoidal sigma weight residual -30.00 -87.98 57.98 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 6687 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.660 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 33.650 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.160 ------------------------------------------------------------------------------- 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 : 16.017 88.104 4056 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 *********************** 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 : 1.104 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2096 time to fit residues: 50.0366 Evaluate side-chains 136 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4784 ------------------------------------------------------------------------------- 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: 0.7920 moved from start: 0.1143 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= 0.219 Angle : 0.548 7.354 15238 Z= 0.272 Chirality : 0.039 0.159 1812 Planarity : 0.004 0.049 1908 Dihedral : 10.069 67.196 1676 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.71 % Allowed : 8.02 % Favored : 91.27 % 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: -0.26 (0.22), residues: 1437 helix: 0.86 (0.17), residues: 877 sheet: -1.56 (0.63), residues: 72 loop : -1.86 (0.25), residues: 488 *********************** 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 156 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 148 time to evaluate : 1.311 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 152 average time/residue: 0.2257 time to fit residues: 50.1171 Evaluate side-chains 141 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 136 time to evaluate : 1.224 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1030 time to fit residues: 2.5361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 108 optimal weight: 9.9990 chunk 88 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 130 optimal weight: 0.0070 chunk 140 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 104 optimal weight: 1.9990 overall best weight: 1.5202 ------------------------------------------------------------------------------- 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: 0.7958 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11225 Z= 0.224 Angle : 0.543 9.012 15238 Z= 0.268 Chirality : 0.039 0.198 1812 Planarity : 0.004 0.051 1908 Dihedral : 9.432 68.230 1676 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.88 % Allowed : 11.02 % Favored : 88.10 % 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: -0.03 (0.22), residues: 1437 helix: 1.09 (0.17), residues: 861 sheet: -1.54 (0.64), residues: 73 loop : -1.74 (0.25), residues: 503 *********************** 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 159 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 149 time to evaluate : 1.818 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 151 average time/residue: 0.2273 time to fit residues: 51.0219 Evaluate side-chains 141 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 135 time to evaluate : 1.221 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1154 time to fit residues: 2.8911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 0.9990 chunk 97 optimal weight: 0.0010 chunk 67 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 130 optimal weight: 0.3980 chunk 138 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- 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: 0.7922 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11225 Z= 0.150 Angle : 0.498 9.085 15238 Z= 0.245 Chirality : 0.038 0.187 1812 Planarity : 0.003 0.037 1908 Dihedral : 8.852 68.184 1676 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.88 % Allowed : 12.61 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.22), residues: 1437 helix: 1.30 (0.18), residues: 859 sheet: -1.53 (0.65), residues: 73 loop : -1.69 (0.26), residues: 505 *********************** 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 151 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 141 time to evaluate : 1.424 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 147 average time/residue: 0.2267 time to fit residues: 49.0569 Evaluate side-chains 136 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 129 time to evaluate : 1.185 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1036 time to fit residues: 3.0074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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: 0.1667 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= 0.185 Angle : 0.508 7.900 15238 Z= 0.251 Chirality : 0.038 0.192 1812 Planarity : 0.003 0.035 1908 Dihedral : 8.511 68.196 1676 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.71 % Allowed : 14.11 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.22), residues: 1437 helix: 1.32 (0.18), residues: 861 sheet: -1.55 (0.65), residues: 73 loop : -1.58 (0.26), residues: 503 *********************** 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 145 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 1.201 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 142 average time/residue: 0.2230 time to fit residues: 46.7337 Evaluate side-chains 135 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 131 time to evaluate : 1.197 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1111 time to fit residues: 2.4239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 0.8980 chunk 124 optimal weight: 20.0000 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7932 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11225 Z= 0.164 Angle : 0.500 8.155 15238 Z= 0.246 Chirality : 0.038 0.210 1812 Planarity : 0.003 0.034 1908 Dihedral : 8.201 68.203 1676 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.88 % Allowed : 14.37 % Favored : 84.74 % 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: 0.36 (0.22), residues: 1437 helix: 1.43 (0.18), residues: 855 sheet: -1.55 (0.65), residues: 73 loop : -1.57 (0.26), residues: 509 *********************** 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 141 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 131 time to evaluate : 1.252 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 137 average time/residue: 0.2185 time to fit residues: 44.1720 Evaluate side-chains 130 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 125 time to evaluate : 1.333 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1160 time to fit residues: 2.7693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 78 optimal weight: 3.9990 chunk 101 optimal weight: 0.0000 chunk 116 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 86 optimal weight: 40.0000 chunk 84 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11225 Z= 0.213 Angle : 0.521 8.351 15238 Z= 0.260 Chirality : 0.039 0.214 1812 Planarity : 0.004 0.043 1908 Dihedral : 8.198 68.499 1676 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.26 % Allowed : 15.26 % Favored : 84.48 % 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: 0.30 (0.22), residues: 1437 helix: 1.34 (0.18), residues: 861 sheet: -1.55 (0.66), residues: 73 loop : -1.56 (0.26), residues: 503 *********************** 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 142 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 139 time to evaluate : 1.500 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 141 average time/residue: 0.2491 time to fit residues: 52.1796 Evaluate side-chains 133 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 1.214 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1032 time to fit residues: 2.0271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 87 optimal weight: 20.0000 chunk 93 optimal weight: 30.0000 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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: 0.7957 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11225 Z= 0.190 Angle : 0.527 8.821 15238 Z= 0.258 Chirality : 0.039 0.227 1812 Planarity : 0.003 0.036 1908 Dihedral : 8.088 68.619 1676 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.53 % Allowed : 15.96 % Favored : 83.51 % 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: 0.32 (0.22), residues: 1437 helix: 1.35 (0.18), residues: 860 sheet: -1.63 (0.63), residues: 78 loop : -1.52 (0.26), residues: 499 *********************** 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 139 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 1.179 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 137 average time/residue: 0.2276 time to fit residues: 46.4972 Evaluate side-chains 131 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 1.152 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1124 time to fit residues: 2.3949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.7946 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11225 Z= 0.171 Angle : 0.520 9.814 15238 Z= 0.257 Chirality : 0.039 0.228 1812 Planarity : 0.003 0.036 1908 Dihedral : 7.925 68.518 1676 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.26 % Allowed : 16.05 % 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: 0.37 (0.22), residues: 1437 helix: 1.38 (0.18), residues: 864 sheet: -1.62 (0.63), residues: 78 loop : -1.48 (0.26), residues: 495 *********************** 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 138 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 135 time to evaluate : 1.206 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 137 average time/residue: 0.2152 time to fit residues: 43.9877 Evaluate side-chains 132 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 1.075 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1033 time to fit residues: 1.9818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 94 optimal weight: 30.0000 chunk 142 optimal weight: 0.3980 chunk 131 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 11 optimal weight: 0.5980 chunk 87 optimal weight: 0.0980 chunk 69 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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: 0.7929 moved from start: 0.1914 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= 0.152 Angle : 0.511 8.525 15238 Z= 0.250 Chirality : 0.038 0.211 1812 Planarity : 0.003 0.036 1908 Dihedral : 7.720 68.267 1676 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.18 % Allowed : 16.49 % 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: 0.44 (0.22), residues: 1437 helix: 1.45 (0.18), residues: 863 sheet: -1.61 (0.63), residues: 78 loop : -1.46 (0.26), residues: 496 ********************** 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 134 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 132 time to evaluate : 1.086 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 133 average time/residue: 0.2066 time to fit residues: 40.9815 Evaluate side-chains 128 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 1.071 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0993 time to fit residues: 1.8433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.0970 chunk 34 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 47 optimal weight: 0.1980 chunk 116 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.145173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.105598 restraints weight = 15032.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.107944 restraints weight = 9406.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.108862 restraints weight = 6721.771| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1935 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= 0.149 Angle : 0.507 9.108 15238 Z= 0.247 Chirality : 0.038 0.203 1812 Planarity : 0.003 0.035 1908 Dihedral : 7.551 67.986 1676 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.18 % Allowed : 16.40 % Favored : 83.42 % 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: 0.50 (0.22), residues: 1437 helix: 1.49 (0.18), residues: 866 sheet: -1.58 (0.62), residues: 78 loop : -1.46 (0.27), residues: 493 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2056.58 seconds wall clock time: 41 minutes 29.83 seconds (2489.83 seconds total)