Starting phenix.real_space_refine on Fri Apr 5 18:04:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfl_37495/04_2024/8wfl_37495_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfl_37495/04_2024/8wfl_37495.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfl_37495/04_2024/8wfl_37495_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfl_37495/04_2024/8wfl_37495_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfl_37495/04_2024/8wfl_37495_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfl_37495/04_2024/8wfl_37495.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfl_37495/04_2024/8wfl_37495.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfl_37495/04_2024/8wfl_37495_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfl_37495/04_2024/8wfl_37495_updated.pdb" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.145 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 S 35 5.16 5 Cl 1 4.86 5 C 2944 2.51 5 N 695 2.21 5 O 738 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 54": "OE1" <-> "OE2" Residue "A TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 225": "OD1" <-> "OD2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 288": "OD1" <-> "OD2" Residue "A TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 606": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 4414 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4388 Classifications: {'peptide': 552} Link IDs: {'PTRANS': 25, 'TRANS': 526} Chain breaks: 1 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'W5X': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.07, per 1000 atoms: 0.70 Number of scatterers: 4414 At special positions: 0 Unit cell: (85.28, 70.52, 91.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 35 16.00 F 1 9.00 O 738 8.00 N 695 7.00 C 2944 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 175 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 766.3 milliseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1006 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 0 sheets defined 63.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 52 through 63 Processing helix chain 'A' and resid 66 through 78 removed outlier: 3.567A pdb=" N TRP A 70 " --> pdb=" O GLY A 67 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ARG A 71 " --> pdb=" O ASN A 68 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N PHE A 72 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 82 through 94 removed outlier: 3.875A pdb=" N MET A 85 " --> pdb=" O GLY A 82 " (cutoff:3.500A) Proline residue: A 87 - end of helix removed outlier: 4.060A pdb=" N ILE A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 110 Processing helix chain 'A' and resid 116 through 119 Processing helix chain 'A' and resid 124 through 156 removed outlier: 4.302A pdb=" N VAL A 134 " --> pdb=" O MET A 131 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE A 138 " --> pdb=" O SER A 135 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR A 142 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASN A 143 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL A 144 " --> pdb=" O TYR A 141 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE A 154 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER A 155 " --> pdb=" O TYR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 217 Processing helix chain 'A' and resid 234 through 250 Processing helix chain 'A' and resid 262 through 280 Proline residue: A 269 - end of helix Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 304 through 317 Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.808A pdb=" N MET A 328 " --> pdb=" O GLY A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 371 removed outlier: 3.613A pdb=" N ILE A 344 " --> pdb=" O ARG A 340 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE A 363 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 390 through 396 removed outlier: 4.574A pdb=" N LEU A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 433 removed outlier: 4.705A pdb=" N LEU A 405 " --> pdb=" O PRO A 401 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N CYS A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 457 Processing helix chain 'A' and resid 459 through 462 Processing helix chain 'A' and resid 466 through 476 Processing helix chain 'A' and resid 480 through 495 removed outlier: 3.690A pdb=" N MET A 494 " --> pdb=" O CYS A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 510 Processing helix chain 'A' and resid 516 through 523 removed outlier: 4.166A pdb=" N ILE A 520 " --> pdb=" O LEU A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 539 Processing helix chain 'A' and resid 553 through 575 removed outlier: 4.497A pdb=" N ILE A 558 " --> pdb=" O TRP A 554 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N CYS A 569 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) Proline residue: A 571 - end of helix removed outlier: 4.241A pdb=" N ALA A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N MET A 575 " --> pdb=" O PRO A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 591 211 hydrogen bonds defined for protein. 531 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 646 1.27 - 1.41: 1323 1.41 - 1.54: 2530 1.54 - 1.68: 4 1.68 - 1.82: 54 Bond restraints: 4557 Sorted by residual: bond pdb=" C14 W5X A 701 " pdb=" N04 W5X A 701 " ideal model delta sigma weight residual 1.470 1.133 0.337 2.00e-02 2.50e+03 2.85e+02 bond pdb=" C22 W5X A 701 " pdb=" C25 W5X A 701 " ideal model delta sigma weight residual 1.389 1.535 -0.146 2.00e-02 2.50e+03 5.33e+01 bond pdb=" C23 W5X A 701 " pdb=" C25 W5X A 701 " ideal model delta sigma weight residual 1.389 1.525 -0.136 2.00e-02 2.50e+03 4.65e+01 bond pdb=" C20 W5X A 701 " pdb=" C23 W5X A 701 " ideal model delta sigma weight residual 1.392 1.523 -0.131 2.00e-02 2.50e+03 4.30e+01 bond pdb=" C17 W5X A 701 " pdb=" C20 W5X A 701 " ideal model delta sigma weight residual 1.389 1.518 -0.129 2.00e-02 2.50e+03 4.16e+01 ... (remaining 4552 not shown) Histogram of bond angle deviations from ideal: 59.81 - 77.70: 3 77.70 - 95.59: 0 95.59 - 113.48: 2506 113.48 - 131.37: 3690 131.37 - 149.25: 18 Bond angle restraints: 6217 Sorted by residual: angle pdb=" C16 W5X A 701 " pdb=" C18 W5X A 701 " pdb=" C21 W5X A 701 " ideal model delta sigma weight residual 110.16 126.17 -16.01 3.00e+00 1.11e-01 2.85e+01 angle pdb=" C16 W5X A 701 " pdb=" C18 W5X A 701 " pdb=" N06 W5X A 701 " ideal model delta sigma weight residual 137.64 124.20 13.44 3.00e+00 1.11e-01 2.01e+01 angle pdb=" C15 W5X A 701 " pdb=" C17 W5X A 701 " pdb=" C19 W5X A 701 " ideal model delta sigma weight residual 99.99 112.19 -12.20 3.00e+00 1.11e-01 1.65e+01 angle pdb=" C15 W5X A 701 " pdb=" C17 W5X A 701 " pdb=" C20 W5X A 701 " ideal model delta sigma weight residual 116.88 126.56 -9.68 3.00e+00 1.11e-01 1.04e+01 angle pdb=" C13 W5X A 701 " pdb=" N05 W5X A 701 " pdb=" C16 W5X A 701 " ideal model delta sigma weight residual 119.82 128.55 -8.73 3.00e+00 1.11e-01 8.46e+00 ... (remaining 6212 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 2192 17.77 - 35.54: 289 35.54 - 53.32: 68 53.32 - 71.09: 13 71.09 - 88.86: 5 Dihedral angle restraints: 2567 sinusoidal: 977 harmonic: 1590 Sorted by residual: dihedral pdb=" CA PRO A 401 " pdb=" C PRO A 401 " pdb=" N LEU A 402 " pdb=" CA LEU A 402 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ALA A 321 " pdb=" C ALA A 321 " pdb=" N TRP A 322 " pdb=" CA TRP A 322 " ideal model delta harmonic sigma weight residual 180.00 163.66 16.34 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CB GLU A 433 " pdb=" CG GLU A 433 " pdb=" CD GLU A 433 " pdb=" OE1 GLU A 433 " ideal model delta sinusoidal sigma weight residual 0.00 -88.78 88.78 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 2564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 627 0.075 - 0.150: 52 0.150 - 0.225: 1 0.225 - 0.301: 1 0.301 - 0.376: 3 Chirality restraints: 684 Sorted by residual: chirality pdb=" C09 W5X A 701 " pdb=" C08 W5X A 701 " pdb=" C10 W5X A 701 " pdb=" C12 W5X A 701 " both_signs ideal model delta sigma weight residual True 2.24 -1.87 0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" C08 W5X A 701 " pdb=" C09 W5X A 701 " pdb=" C10 W5X A 701 " pdb=" C11 W5X A 701 " both_signs ideal model delta sigma weight residual True 1.54 1.19 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" C10 W5X A 701 " pdb=" C08 W5X A 701 " pdb=" C09 W5X A 701 " pdb=" C13 W5X A 701 " both_signs ideal model delta sigma weight residual True 2.78 2.44 0.34 2.00e-01 2.50e+01 2.95e+00 ... (remaining 681 not shown) Planarity restraints: 762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 170 " 0.012 2.00e-02 2.50e+03 1.26e-02 3.96e+00 pdb=" CG TRP A 170 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP A 170 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 170 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 170 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 170 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 170 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 170 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 170 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 170 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 86 " -0.025 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO A 87 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 87 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 87 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 268 " 0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO A 269 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 269 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 269 " 0.020 5.00e-02 4.00e+02 ... (remaining 759 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 825 2.76 - 3.29: 4328 3.29 - 3.83: 7362 3.83 - 4.36: 8277 4.36 - 4.90: 14242 Nonbonded interactions: 35034 Sorted by model distance: nonbonded pdb=" OG SER A 257 " pdb=" OE2 GLU A 424 " model vdw 2.223 2.440 nonbonded pdb=" O PRO A 602 " pdb=" NH2 ARG A 608 " model vdw 2.291 2.520 nonbonded pdb=" OG1 THR A 172 " pdb=" OE2 GLU A 213 " model vdw 2.311 2.440 nonbonded pdb=" CG2 VAL A 178 " pdb=" CD1 LEU A 371 " model vdw 2.312 3.880 nonbonded pdb=" OH TYR A 476 " pdb=" OH TYR A 541 " model vdw 2.326 2.440 ... (remaining 35029 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 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: 3.760 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.200 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 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 : 0.008 0.337 4557 Z= 0.550 Angle : 0.729 16.012 6217 Z= 0.341 Chirality : 0.048 0.376 684 Planarity : 0.004 0.039 762 Dihedral : 17.258 88.862 1558 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.21 % Allowed : 29.98 % Favored : 69.81 % 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 (0.37), residues: 548 helix: 0.78 (0.29), residues: 354 sheet: None (None), residues: 0 loop : -2.20 (0.45), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 170 HIS 0.003 0.001 HIS A 370 PHE 0.016 0.001 PHE A 420 TYR 0.023 0.001 TYR A 62 ARG 0.003 0.000 ARG A 119 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.443 Fit side-chains REVERT: A 62 TYR cc_start: 0.8623 (t80) cc_final: 0.8376 (t80) REVERT: A 404 SER cc_start: 0.8489 (p) cc_final: 0.8254 (m) REVERT: A 433 GLU cc_start: 0.7952 (tp30) cc_final: 0.7305 (tt0) outliers start: 1 outliers final: 1 residues processed: 102 average time/residue: 0.1593 time to fit residues: 20.7510 Evaluate side-chains 93 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.0594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4557 Z= 0.221 Angle : 0.589 11.079 6217 Z= 0.290 Chirality : 0.042 0.178 684 Planarity : 0.004 0.038 762 Dihedral : 6.051 81.045 615 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 7.92 % Allowed : 24.20 % Favored : 67.88 % 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: -0.66 (0.37), residues: 548 helix: 0.48 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -2.31 (0.46), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 322 HIS 0.003 0.001 HIS A 370 PHE 0.024 0.001 PHE A 109 TYR 0.017 0.001 TYR A 141 ARG 0.002 0.000 ARG A 611 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 94 time to evaluate : 0.485 Fit side-chains REVERT: A 62 TYR cc_start: 0.8805 (t80) cc_final: 0.8534 (t80) REVERT: A 404 SER cc_start: 0.8485 (p) cc_final: 0.8218 (m) REVERT: A 433 GLU cc_start: 0.7997 (tp30) cc_final: 0.7296 (tt0) REVERT: A 516 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8116 (mt) outliers start: 37 outliers final: 26 residues processed: 111 average time/residue: 0.1531 time to fit residues: 21.9951 Evaluate side-chains 115 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 88 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 54 optimal weight: 0.3980 chunk 44 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.0668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4557 Z= 0.166 Angle : 0.557 10.303 6217 Z= 0.273 Chirality : 0.040 0.197 684 Planarity : 0.004 0.038 762 Dihedral : 5.912 79.126 615 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 6.64 % Allowed : 24.63 % Favored : 68.74 % 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: -0.55 (0.37), residues: 548 helix: 0.55 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -2.24 (0.47), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 322 HIS 0.002 0.001 HIS A 607 PHE 0.018 0.001 PHE A 109 TYR 0.017 0.001 TYR A 141 ARG 0.002 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 93 time to evaluate : 0.464 Fit side-chains REVERT: A 62 TYR cc_start: 0.8771 (t80) cc_final: 0.8502 (t80) REVERT: A 78 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.6788 (ttp-110) REVERT: A 433 GLU cc_start: 0.7974 (tp30) cc_final: 0.7285 (tt0) outliers start: 31 outliers final: 23 residues processed: 110 average time/residue: 0.1551 time to fit residues: 21.7788 Evaluate side-chains 115 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 91 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4557 Z= 0.187 Angle : 0.556 10.314 6217 Z= 0.273 Chirality : 0.040 0.207 684 Planarity : 0.004 0.038 762 Dihedral : 5.902 78.808 615 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 6.85 % Allowed : 24.41 % Favored : 68.74 % 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: -0.55 (0.37), residues: 548 helix: 0.53 (0.28), residues: 366 sheet: None (None), residues: 0 loop : -2.21 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 322 HIS 0.002 0.001 HIS A 607 PHE 0.020 0.001 PHE A 109 TYR 0.016 0.001 TYR A 141 ARG 0.002 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 92 time to evaluate : 0.462 Fit side-chains REVERT: A 424 GLU cc_start: 0.7578 (tp30) cc_final: 0.7261 (mm-30) REVERT: A 433 GLU cc_start: 0.8003 (tp30) cc_final: 0.7314 (tt0) outliers start: 32 outliers final: 25 residues processed: 110 average time/residue: 0.1435 time to fit residues: 20.4869 Evaluate side-chains 113 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 88 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 39 optimal weight: 0.0060 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 540 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4557 Z= 0.164 Angle : 0.542 10.112 6217 Z= 0.267 Chirality : 0.039 0.169 684 Planarity : 0.004 0.036 762 Dihedral : 5.783 76.410 615 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 7.49 % Allowed : 24.20 % Favored : 68.31 % 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: -0.47 (0.38), residues: 548 helix: 0.59 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -2.16 (0.48), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 322 HIS 0.002 0.001 HIS A 607 PHE 0.023 0.001 PHE A 109 TYR 0.015 0.001 TYR A 141 ARG 0.003 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 88 time to evaluate : 0.469 Fit side-chains REVERT: A 78 ARG cc_start: 0.7528 (ttm-80) cc_final: 0.6874 (ttp-110) REVERT: A 129 TYR cc_start: 0.7588 (OUTLIER) cc_final: 0.6870 (m-10) REVERT: A 424 GLU cc_start: 0.7594 (tp30) cc_final: 0.7275 (mm-30) REVERT: A 433 GLU cc_start: 0.8007 (tp30) cc_final: 0.7320 (tt0) outliers start: 35 outliers final: 23 residues processed: 108 average time/residue: 0.1417 time to fit residues: 19.9082 Evaluate side-chains 109 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 85 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.0870 chunk 13 optimal weight: 9.9990 chunk 53 optimal weight: 0.0010 chunk 44 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.4564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4557 Z= 0.148 Angle : 0.526 9.969 6217 Z= 0.259 Chirality : 0.038 0.149 684 Planarity : 0.004 0.035 762 Dihedral : 5.622 73.534 615 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 6.21 % Allowed : 24.63 % Favored : 69.16 % 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 (0.38), residues: 548 helix: 0.73 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -2.08 (0.48), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 600 HIS 0.001 0.000 HIS A 381 PHE 0.024 0.001 PHE A 109 TYR 0.015 0.001 TYR A 141 ARG 0.003 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 92 time to evaluate : 0.456 Fit side-chains REVERT: A 78 ARG cc_start: 0.7516 (ttm-80) cc_final: 0.6864 (ttp-110) REVERT: A 129 TYR cc_start: 0.7573 (OUTLIER) cc_final: 0.6828 (m-10) REVERT: A 424 GLU cc_start: 0.7594 (tp30) cc_final: 0.7257 (mm-30) REVERT: A 433 GLU cc_start: 0.8005 (tp30) cc_final: 0.7332 (tt0) outliers start: 29 outliers final: 24 residues processed: 107 average time/residue: 0.1490 time to fit residues: 20.5950 Evaluate side-chains 115 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 90 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN A 540 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4557 Z= 0.165 Angle : 0.544 9.996 6217 Z= 0.265 Chirality : 0.039 0.142 684 Planarity : 0.004 0.034 762 Dihedral : 5.295 72.753 613 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 6.21 % Allowed : 24.41 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.38), residues: 548 helix: 0.75 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -2.05 (0.49), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 600 HIS 0.002 0.000 HIS A 607 PHE 0.026 0.001 PHE A 109 TYR 0.015 0.001 TYR A 141 ARG 0.003 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 90 time to evaluate : 0.472 Fit side-chains REVERT: A 75 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8106 (tm) REVERT: A 78 ARG cc_start: 0.7540 (ttm-80) cc_final: 0.6880 (ttp-110) REVERT: A 129 TYR cc_start: 0.7523 (OUTLIER) cc_final: 0.6821 (m-10) REVERT: A 424 GLU cc_start: 0.7631 (tp30) cc_final: 0.7015 (tp30) REVERT: A 433 GLU cc_start: 0.8014 (tp30) cc_final: 0.7315 (tt0) outliers start: 29 outliers final: 22 residues processed: 104 average time/residue: 0.1547 time to fit residues: 20.8840 Evaluate side-chains 113 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 89 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 49 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4557 Z= 0.155 Angle : 0.547 11.719 6217 Z= 0.263 Chirality : 0.038 0.139 684 Planarity : 0.004 0.034 762 Dihedral : 5.234 71.741 613 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 6.21 % Allowed : 24.20 % Favored : 69.59 % 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: -0.18 (0.38), residues: 548 helix: 0.80 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -2.00 (0.49), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 170 HIS 0.001 0.000 HIS A 607 PHE 0.028 0.001 PHE A 109 TYR 0.014 0.001 TYR A 141 ARG 0.002 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 91 time to evaluate : 0.427 Fit side-chains REVERT: A 78 ARG cc_start: 0.7550 (ttm-80) cc_final: 0.6822 (ttp80) REVERT: A 129 TYR cc_start: 0.7533 (OUTLIER) cc_final: 0.6812 (m-10) REVERT: A 303 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6448 (mp0) REVERT: A 327 THR cc_start: 0.8446 (OUTLIER) cc_final: 0.8063 (m) REVERT: A 424 GLU cc_start: 0.7647 (tp30) cc_final: 0.7059 (tp30) REVERT: A 433 GLU cc_start: 0.7968 (tp30) cc_final: 0.7276 (tt0) REVERT: A 440 LEU cc_start: 0.7168 (mm) cc_final: 0.6886 (mm) outliers start: 29 outliers final: 24 residues processed: 107 average time/residue: 0.1398 time to fit residues: 19.4422 Evaluate side-chains 117 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 90 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 38 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4557 Z= 0.162 Angle : 0.547 11.350 6217 Z= 0.265 Chirality : 0.039 0.137 684 Planarity : 0.004 0.034 762 Dihedral : 5.210 71.254 613 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 6.21 % Allowed : 23.98 % Favored : 69.81 % 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: -0.21 (0.38), residues: 548 helix: 0.77 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -1.99 (0.49), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 600 HIS 0.002 0.000 HIS A 607 PHE 0.029 0.001 PHE A 109 TYR 0.014 0.001 TYR A 141 ARG 0.003 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 89 time to evaluate : 0.477 Fit side-chains REVERT: A 78 ARG cc_start: 0.7557 (ttm-80) cc_final: 0.6842 (ttp-110) REVERT: A 129 TYR cc_start: 0.7542 (OUTLIER) cc_final: 0.6846 (m-10) REVERT: A 303 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6444 (mp0) REVERT: A 327 THR cc_start: 0.8460 (OUTLIER) cc_final: 0.8079 (m) REVERT: A 424 GLU cc_start: 0.7652 (tp30) cc_final: 0.7063 (tp30) REVERT: A 433 GLU cc_start: 0.7977 (tp30) cc_final: 0.7267 (tt0) REVERT: A 440 LEU cc_start: 0.7183 (mm) cc_final: 0.6900 (mm) outliers start: 29 outliers final: 24 residues processed: 104 average time/residue: 0.1484 time to fit residues: 19.9927 Evaluate side-chains 116 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 89 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4557 Z= 0.178 Angle : 0.553 11.332 6217 Z= 0.268 Chirality : 0.039 0.134 684 Planarity : 0.004 0.034 762 Dihedral : 5.224 70.766 613 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 5.57 % Allowed : 24.63 % Favored : 69.81 % 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: -0.23 (0.38), residues: 548 helix: 0.77 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -2.02 (0.49), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 600 HIS 0.002 0.001 HIS A 607 PHE 0.030 0.001 PHE A 109 TYR 0.014 0.001 TYR A 141 ARG 0.002 0.000 ARG A 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 88 time to evaluate : 0.486 Fit side-chains REVERT: A 78 ARG cc_start: 0.7567 (ttm-80) cc_final: 0.6875 (ttp-110) REVERT: A 129 TYR cc_start: 0.7564 (OUTLIER) cc_final: 0.6867 (m-10) REVERT: A 327 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8153 (m) REVERT: A 424 GLU cc_start: 0.7662 (tp30) cc_final: 0.7090 (tp30) REVERT: A 433 GLU cc_start: 0.7978 (tp30) cc_final: 0.7261 (tt0) REVERT: A 440 LEU cc_start: 0.7199 (mm) cc_final: 0.6907 (mm) outliers start: 26 outliers final: 23 residues processed: 103 average time/residue: 0.1397 time to fit residues: 19.0067 Evaluate side-chains 113 residues out of total 467 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 88 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 150 PHE Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 0.5980 chunk 6 optimal weight: 8.9990 chunk 12 optimal weight: 0.0670 chunk 43 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.161428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.150271 restraints weight = 6369.301| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.32 r_work: 0.3686 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4557 Z= 0.177 Angle : 0.561 11.278 6217 Z= 0.271 Chirality : 0.039 0.133 684 Planarity : 0.004 0.035 762 Dihedral : 5.209 70.346 613 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 5.57 % Allowed : 24.84 % Favored : 69.59 % 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: -0.24 (0.38), residues: 548 helix: 0.76 (0.28), residues: 362 sheet: None (None), residues: 0 loop : -2.01 (0.49), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 600 HIS 0.002 0.001 HIS A 607 PHE 0.030 0.001 PHE A 109 TYR 0.014 0.001 TYR A 141 ARG 0.002 0.000 ARG A 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1317.96 seconds wall clock time: 24 minutes 39.90 seconds (1479.90 seconds total)