Starting phenix.real_space_refine on Tue Feb 13 13:15:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9b_15275/02_2024/8a9b_15275.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9b_15275/02_2024/8a9b_15275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9b_15275/02_2024/8a9b_15275.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9b_15275/02_2024/8a9b_15275.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9b_15275/02_2024/8a9b_15275.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9b_15275/02_2024/8a9b_15275.pdb" } resolution = 4.0 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= -0.001 sd= 0.093 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: 4 Type Number sf(0) Gaussians S 8 5.16 5 C 4120 2.51 5 N 1027 2.21 5 O 1231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "B ASP 271": "OD1" <-> "OD2" Residue "B PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 603": "OE1" <-> "OE2" Residue "B PHE 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 719": "OD1" <-> "OD2" Residue "B PHE 854": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6386 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 6386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6386 Classifications: {'peptide': 809} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 786} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 3.87, per 1000 atoms: 0.61 Number of scatterers: 6386 At special positions: 0 Unit cell: (91.41, 103.044, 149.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 8 16.00 O 1231 8.00 N 1027 7.00 C 4120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.3 seconds 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1530 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 6 sheets defined 42.3% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'B' and resid 95 through 106 removed outlier: 3.572A pdb=" N GLY B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 125 removed outlier: 3.820A pdb=" N ALA B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 removed outlier: 3.742A pdb=" N ASN B 255 " --> pdb=" O GLU B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 266 Processing helix chain 'B' and resid 268 through 297 removed outlier: 3.936A pdb=" N GLY B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 304 removed outlier: 4.202A pdb=" N GLN B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 316 Processing helix chain 'B' and resid 319 through 331 Processing helix chain 'B' and resid 334 through 344 Processing helix chain 'B' and resid 353 through 360 removed outlier: 3.966A pdb=" N LEU B 357 " --> pdb=" O THR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 370 Processing helix chain 'B' and resid 376 through 381 Processing helix chain 'B' and resid 383 through 389 Processing helix chain 'B' and resid 396 through 414 removed outlier: 4.462A pdb=" N ASP B 406 " --> pdb=" O GLN B 402 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Proline residue: B 410 - end of helix Processing helix chain 'B' and resid 421 through 431 removed outlier: 3.647A pdb=" N GLN B 431 " --> pdb=" O GLU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 462 Processing helix chain 'B' and resid 465 through 477 removed outlier: 4.038A pdb=" N VAL B 469 " --> pdb=" O MET B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 486 Processing helix chain 'B' and resid 489 through 499 Processing helix chain 'B' and resid 515 through 525 Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 552 through 557 removed outlier: 3.647A pdb=" N ALA B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 582 removed outlier: 3.879A pdb=" N GLU B 569 " --> pdb=" O ASP B 565 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 570 " --> pdb=" O TYR B 566 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA B 573 " --> pdb=" O GLU B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 592 Processing helix chain 'B' and resid 635 through 643 Processing helix chain 'B' and resid 649 through 659 removed outlier: 4.131A pdb=" N THR B 653 " --> pdb=" O ASP B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 674 Processing helix chain 'B' and resid 685 through 689 Processing helix chain 'B' and resid 692 through 700 Processing helix chain 'B' and resid 706 through 717 Processing helix chain 'B' and resid 797 through 816 Processing sheet with id=AA1, first strand: chain 'B' and resid 135 through 137 removed outlier: 4.353A pdb=" N PHE B 157 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR B 187 " --> pdb=" O PHE B 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 141 through 142 removed outlier: 3.618A pdb=" N ASN B 142 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASP B 154 " --> pdb=" O ASN B 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 189 through 190 removed outlier: 3.584A pdb=" N ASN B 190 " --> pdb=" O THR B 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 607 through 609 removed outlier: 3.987A pdb=" N LEU B 614 " --> pdb=" O VAL B 747 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LYS B 618 " --> pdb=" O GLU B 743 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLU B 743 " --> pdb=" O LYS B 618 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ASP B 620 " --> pdb=" O GLY B 741 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLY B 741 " --> pdb=" O ASP B 620 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 736 " --> pdb=" O VAL B 625 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 607 through 609 removed outlier: 3.987A pdb=" N LEU B 614 " --> pdb=" O VAL B 747 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LYS B 618 " --> pdb=" O GLU B 743 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLU B 743 " --> pdb=" O LYS B 618 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ASP B 620 " --> pdb=" O GLY B 741 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLY B 741 " --> pdb=" O ASP B 620 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR B 769 " --> pdb=" O LYS B 739 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLU B 743 " --> pdb=" O GLY B 765 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N GLY B 765 " --> pdb=" O GLU B 743 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N LEU B 745 " --> pdb=" O ILE B 763 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE B 763 " --> pdb=" O LEU B 745 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N VAL B 747 " --> pdb=" O TYR B 761 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N TYR B 761 " --> pdb=" O VAL B 747 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLN B 762 " --> pdb=" O VAL B 829 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL B 829 " --> pdb=" O GLN B 762 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ILE B 764 " --> pdb=" O ILE B 827 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ILE B 827 " --> pdb=" O ILE B 764 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 630 through 632 removed outlier: 3.843A pdb=" N PHE B 630 " --> pdb=" O LEU B 732 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU B 778 " --> pdb=" O THR B 731 " (cutoff:3.500A) 239 hydrogen bonds defined for protein. 687 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: 1.77 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2007 1.34 - 1.45: 795 1.45 - 1.57: 3677 1.57 - 1.69: 0 1.69 - 1.80: 16 Bond restraints: 6495 Sorted by residual: bond pdb=" CA THR B 414 " pdb=" C THR B 414 " ideal model delta sigma weight residual 1.524 1.557 -0.033 1.59e-02 3.96e+03 4.39e+00 bond pdb=" CG1 ILE B 289 " pdb=" CD1 ILE B 289 " ideal model delta sigma weight residual 1.513 1.450 0.063 3.90e-02 6.57e+02 2.65e+00 bond pdb=" CG LEU B 797 " pdb=" CD1 LEU B 797 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.10e+00 bond pdb=" CB PRO B 375 " pdb=" CG PRO B 375 " ideal model delta sigma weight residual 1.506 1.458 0.048 3.90e-02 6.57e+02 1.54e+00 bond pdb=" CG PRO B 375 " pdb=" CD PRO B 375 " ideal model delta sigma weight residual 1.512 1.479 0.033 2.70e-02 1.37e+03 1.45e+00 ... (remaining 6490 not shown) Histogram of bond angle deviations from ideal: 100.24 - 109.18: 371 109.18 - 118.12: 4540 118.12 - 127.06: 3809 127.06 - 136.00: 29 136.00 - 144.95: 1 Bond angle restraints: 8750 Sorted by residual: angle pdb=" C ILE B 374 " pdb=" N PRO B 375 " pdb=" CD PRO B 375 " ideal model delta sigma weight residual 120.60 101.54 19.06 2.20e+00 2.07e-01 7.51e+01 angle pdb=" N PRO B 61 " pdb=" CA PRO B 61 " pdb=" CB PRO B 61 " ideal model delta sigma weight residual 103.25 111.43 -8.18 1.05e+00 9.07e-01 6.07e+01 angle pdb=" C ILE B 374 " pdb=" N PRO B 375 " pdb=" CA PRO B 375 " ideal model delta sigma weight residual 127.00 144.95 -17.95 2.40e+00 1.74e-01 5.59e+01 angle pdb=" C ILE B 374 " pdb=" CA ILE B 374 " pdb=" CB ILE B 374 " ideal model delta sigma weight residual 111.36 120.22 -8.86 1.82e+00 3.02e-01 2.37e+01 angle pdb=" C PHE B 437 " pdb=" N ASP B 438 " pdb=" CA ASP B 438 " ideal model delta sigma weight residual 121.54 129.80 -8.26 1.91e+00 2.74e-01 1.87e+01 ... (remaining 8745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.67: 3475 16.67 - 33.35: 373 33.35 - 50.02: 79 50.02 - 66.70: 8 66.70 - 83.37: 12 Dihedral angle restraints: 3947 sinusoidal: 1589 harmonic: 2358 Sorted by residual: dihedral pdb=" CA ILE B 374 " pdb=" C ILE B 374 " pdb=" N PRO B 375 " pdb=" CA PRO B 375 " ideal model delta harmonic sigma weight residual 0.00 -34.11 34.11 0 5.00e+00 4.00e-02 4.65e+01 dihedral pdb=" CA ILE B 632 " pdb=" C ILE B 632 " pdb=" N LYS B 633 " pdb=" CA LYS B 633 " ideal model delta harmonic sigma weight residual -180.00 -148.44 -31.56 0 5.00e+00 4.00e-02 3.98e+01 dihedral pdb=" CA GLU B 416 " pdb=" C GLU B 416 " pdb=" N LYS B 417 " pdb=" CA LYS B 417 " ideal model delta harmonic sigma weight residual 180.00 153.22 26.78 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 3944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 937 0.096 - 0.191: 57 0.191 - 0.287: 4 0.287 - 0.383: 0 0.383 - 0.478: 1 Chirality restraints: 999 Sorted by residual: chirality pdb=" CB ILE B 374 " pdb=" CA ILE B 374 " pdb=" CG1 ILE B 374 " pdb=" CG2 ILE B 374 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CB ILE B 289 " pdb=" CA ILE B 289 " pdb=" CG1 ILE B 289 " pdb=" CG2 ILE B 289 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB THR B 610 " pdb=" CA THR B 610 " pdb=" OG1 THR B 610 " pdb=" CG2 THR B 610 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 996 not shown) Planarity restraints: 1119 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 686 " 0.044 5.00e-02 4.00e+02 6.76e-02 7.32e+00 pdb=" N PRO B 687 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 687 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 687 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 374 " 0.038 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO B 375 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 375 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 375 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 852 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO B 853 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 853 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 853 " 0.025 5.00e-02 4.00e+02 ... (remaining 1116 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 168 2.67 - 3.23: 6610 3.23 - 3.79: 9933 3.79 - 4.34: 13463 4.34 - 4.90: 20822 Nonbonded interactions: 50996 Sorted by model distance: nonbonded pdb=" O ALA B 470 " pdb=" OG1 THR B 473 " model vdw 2.113 2.440 nonbonded pdb=" OG SER B 311 " pdb=" O LEU B 484 " model vdw 2.153 2.440 nonbonded pdb=" OE1 GLU B 306 " pdb=" NZ LYS B 575 " model vdw 2.190 2.520 nonbonded pdb=" OE1 GLU B 758 " pdb=" OG SER B 838 " model vdw 2.211 2.440 nonbonded pdb=" OG1 THR B 768 " pdb=" O PHE B 823 " model vdw 2.220 2.440 ... (remaining 50991 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.880 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 21.170 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5803 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 0.063 6495 Z= 0.276 Angle : 0.877 19.061 8750 Z= 0.459 Chirality : 0.051 0.478 999 Planarity : 0.005 0.068 1119 Dihedral : 14.890 83.373 2417 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 1.00 % Allowed : 14.82 % Favored : 84.18 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.13 % 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: -3.17 (0.28), residues: 803 helix: -0.88 (0.28), residues: 328 sheet: -2.16 (0.78), residues: 50 loop : -3.23 (0.27), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 805 HIS 0.003 0.001 HIS B 216 PHE 0.023 0.002 PHE B 578 TYR 0.029 0.002 TYR B 740 ARG 0.007 0.001 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 294 MET cc_start: 0.5566 (mtt) cc_final: 0.5230 (mmp) REVERT: B 447 LEU cc_start: 0.7382 (mm) cc_final: 0.7135 (mm) REVERT: B 633 LYS cc_start: 0.8057 (tptm) cc_final: 0.7845 (tptp) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1885 time to fit residues: 18.8893 Evaluate side-chains 46 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 62 optimal weight: 0.0170 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 72 optimal weight: 0.1980 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5832 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6495 Z= 0.223 Angle : 0.761 10.334 8750 Z= 0.392 Chirality : 0.048 0.501 999 Planarity : 0.004 0.054 1119 Dihedral : 6.205 36.149 838 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.87 % Allowed : 13.95 % Favored : 85.18 % Rotamer: Outliers : 1.00 % Allowed : 9.29 % Favored : 89.71 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: -3.05 (0.28), residues: 803 helix: -0.83 (0.28), residues: 329 sheet: -2.55 (0.76), residues: 51 loop : -3.05 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 121 HIS 0.002 0.001 HIS B 266 PHE 0.028 0.002 PHE B 854 TYR 0.016 0.001 TYR B 187 ARG 0.005 0.001 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 185 PHE cc_start: 0.4438 (t80) cc_final: 0.4078 (t80) REVERT: B 294 MET cc_start: 0.5653 (mtt) cc_final: 0.5177 (mmp) REVERT: B 447 LEU cc_start: 0.7417 (mm) cc_final: 0.7200 (mm) REVERT: B 640 MET cc_start: 0.7479 (ptm) cc_final: 0.7061 (ptm) outliers start: 7 outliers final: 3 residues processed: 62 average time/residue: 0.1807 time to fit residues: 15.9913 Evaluate side-chains 50 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 785 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 78 optimal weight: 0.0170 chunk 64 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 849 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5867 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6495 Z= 0.218 Angle : 0.753 9.982 8750 Z= 0.384 Chirality : 0.047 0.505 999 Planarity : 0.004 0.058 1119 Dihedral : 6.137 35.058 838 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.87 % Allowed : 13.82 % Favored : 85.31 % Rotamer: Outliers : 1.86 % Allowed : 13.57 % Favored : 84.57 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.28), residues: 803 helix: -0.74 (0.28), residues: 331 sheet: -2.78 (0.75), residues: 49 loop : -2.98 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 805 HIS 0.002 0.001 HIS B 216 PHE 0.026 0.002 PHE B 854 TYR 0.014 0.001 TYR B 187 ARG 0.004 0.001 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 48 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 447 LEU cc_start: 0.7387 (mm) cc_final: 0.7161 (mm) outliers start: 13 outliers final: 6 residues processed: 59 average time/residue: 0.1402 time to fit residues: 12.5761 Evaluate side-chains 49 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 785 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 0.0870 chunk 77 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 69 optimal weight: 0.0970 chunk 20 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5850 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6495 Z= 0.201 Angle : 0.739 13.033 8750 Z= 0.373 Chirality : 0.045 0.243 999 Planarity : 0.004 0.061 1119 Dihedral : 5.915 27.208 838 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.75 % Allowed : 13.82 % Favored : 85.43 % Rotamer: Outliers : 1.71 % Allowed : 16.14 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.29), residues: 803 helix: -0.73 (0.28), residues: 337 sheet: -3.12 (0.68), residues: 52 loop : -2.92 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 805 HIS 0.002 0.001 HIS B 216 PHE 0.038 0.002 PHE B 111 TYR 0.012 0.001 TYR B 187 ARG 0.005 0.001 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 49 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 447 LEU cc_start: 0.7206 (mm) cc_final: 0.6868 (mm) REVERT: B 640 MET cc_start: 0.7474 (ptm) cc_final: 0.7118 (ptm) REVERT: B 669 ASP cc_start: 0.6082 (m-30) cc_final: 0.5872 (p0) outliers start: 12 outliers final: 8 residues processed: 59 average time/residue: 0.1378 time to fit residues: 12.3382 Evaluate side-chains 50 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 785 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 53 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5971 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 6495 Z= 0.262 Angle : 0.756 9.711 8750 Z= 0.386 Chirality : 0.046 0.227 999 Planarity : 0.004 0.064 1119 Dihedral : 6.098 27.155 838 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 22.39 Ramachandran Plot: Outliers : 0.75 % Allowed : 15.07 % Favored : 84.18 % Rotamer: Outliers : 2.29 % Allowed : 17.43 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -3.02 (0.28), residues: 803 helix: -0.74 (0.28), residues: 329 sheet: -2.86 (0.77), residues: 42 loop : -3.06 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 121 HIS 0.002 0.001 HIS B 216 PHE 0.035 0.002 PHE B 111 TYR 0.012 0.001 TYR B 187 ARG 0.006 0.001 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 48 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 LYS cc_start: 0.7286 (OUTLIER) cc_final: 0.6926 (tptp) REVERT: B 447 LEU cc_start: 0.7394 (mm) cc_final: 0.7115 (mm) REVERT: B 465 MET cc_start: 0.4673 (OUTLIER) cc_final: 0.3638 (mtm) REVERT: B 669 ASP cc_start: 0.6338 (m-30) cc_final: 0.6111 (p0) outliers start: 16 outliers final: 10 residues processed: 60 average time/residue: 0.1765 time to fit residues: 14.9992 Evaluate side-chains 54 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 42 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 785 LYS Chi-restraints excluded: chain B residue 837 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 35 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.0970 chunk 74 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5953 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6495 Z= 0.228 Angle : 0.733 10.144 8750 Z= 0.373 Chirality : 0.045 0.231 999 Planarity : 0.004 0.065 1119 Dihedral : 6.072 26.519 838 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 21.92 Ramachandran Plot: Outliers : 0.75 % Allowed : 14.94 % Favored : 84.31 % Rotamer: Outliers : 3.43 % Allowed : 19.14 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -3.09 (0.27), residues: 803 helix: -0.83 (0.27), residues: 335 sheet: -3.16 (0.78), residues: 34 loop : -3.09 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 121 HIS 0.002 0.001 HIS B 216 PHE 0.032 0.002 PHE B 111 TYR 0.011 0.001 TYR B 751 ARG 0.004 0.001 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 56 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 LYS cc_start: 0.7154 (OUTLIER) cc_final: 0.6901 (tptp) REVERT: B 447 LEU cc_start: 0.7478 (mm) cc_final: 0.6520 (tp) outliers start: 24 outliers final: 16 residues processed: 75 average time/residue: 0.1449 time to fit residues: 16.0553 Evaluate side-chains 64 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 47 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 785 LYS Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 851 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5962 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6495 Z= 0.216 Angle : 0.742 10.816 8750 Z= 0.375 Chirality : 0.045 0.241 999 Planarity : 0.004 0.065 1119 Dihedral : 6.032 26.367 838 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.75 % Allowed : 15.69 % Favored : 83.56 % Rotamer: Outliers : 3.29 % Allowed : 20.43 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -3.07 (0.28), residues: 803 helix: -0.90 (0.27), residues: 338 sheet: -3.02 (0.81), residues: 34 loop : -3.03 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 121 HIS 0.001 0.001 HIS B 216 PHE 0.034 0.002 PHE B 111 TYR 0.011 0.001 TYR B 751 ARG 0.007 0.001 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 49 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 LYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6925 (tptp) REVERT: B 640 MET cc_start: 0.7409 (ptm) cc_final: 0.7052 (ptm) REVERT: B 740 TYR cc_start: 0.7879 (OUTLIER) cc_final: 0.7454 (t80) outliers start: 23 outliers final: 18 residues processed: 68 average time/residue: 0.1591 time to fit residues: 15.9898 Evaluate side-chains 64 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 44 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 740 TYR Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 785 LYS Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 851 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 7 optimal weight: 0.3980 chunk 60 optimal weight: 0.1980 chunk 70 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5925 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6495 Z= 0.190 Angle : 0.721 9.850 8750 Z= 0.363 Chirality : 0.044 0.206 999 Planarity : 0.004 0.065 1119 Dihedral : 5.909 25.751 838 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.75 % Allowed : 13.95 % Favored : 85.31 % Rotamer: Outliers : 2.86 % Allowed : 22.14 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.28), residues: 803 helix: -0.80 (0.28), residues: 336 sheet: -2.93 (0.82), residues: 34 loop : -2.94 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 121 HIS 0.001 0.000 HIS B 216 PHE 0.033 0.002 PHE B 111 TYR 0.009 0.001 TYR B 751 ARG 0.005 0.001 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 48 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 640 MET cc_start: 0.7400 (ptm) cc_final: 0.7032 (ptm) REVERT: B 740 TYR cc_start: 0.7843 (OUTLIER) cc_final: 0.7381 (t80) outliers start: 20 outliers final: 14 residues processed: 64 average time/residue: 0.1609 time to fit residues: 15.2486 Evaluate side-chains 61 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 46 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 740 TYR Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 785 LYS Chi-restraints excluded: chain B residue 837 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5990 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6495 Z= 0.227 Angle : 0.758 11.186 8750 Z= 0.383 Chirality : 0.046 0.236 999 Planarity : 0.004 0.065 1119 Dihedral : 6.022 25.674 838 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 22.00 Ramachandran Plot: Outliers : 0.75 % Allowed : 14.94 % Favored : 84.31 % Rotamer: Outliers : 2.86 % Allowed : 22.14 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -3.05 (0.28), residues: 803 helix: -0.91 (0.28), residues: 337 sheet: -2.88 (0.81), residues: 34 loop : -2.99 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 121 HIS 0.001 0.001 HIS B 216 PHE 0.034 0.002 PHE B 111 TYR 0.011 0.001 TYR B 751 ARG 0.005 0.001 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 49 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 640 MET cc_start: 0.7538 (ptm) cc_final: 0.7168 (ptm) REVERT: B 650 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7249 (tp) REVERT: B 740 TYR cc_start: 0.7849 (OUTLIER) cc_final: 0.7417 (t80) outliers start: 20 outliers final: 17 residues processed: 65 average time/residue: 0.1607 time to fit residues: 15.2720 Evaluate side-chains 65 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 46 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 740 TYR Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 785 LYS Chi-restraints excluded: chain B residue 817 PHE Chi-restraints excluded: chain B residue 837 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 6.9990 chunk 52 optimal weight: 0.0270 chunk 79 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 0.0000 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.5042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5949 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6495 Z= 0.192 Angle : 0.737 10.585 8750 Z= 0.370 Chirality : 0.045 0.228 999 Planarity : 0.004 0.067 1119 Dihedral : 5.920 25.684 838 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.75 % Allowed : 13.82 % Favored : 85.43 % Rotamer: Outliers : 2.86 % Allowed : 22.43 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.28), residues: 803 helix: -0.86 (0.28), residues: 335 sheet: -2.79 (0.80), residues: 34 loop : -2.96 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 121 HIS 0.001 0.000 HIS B 216 PHE 0.034 0.002 PHE B 111 TYR 0.011 0.001 TYR B 206 ARG 0.004 0.001 ARG B 140 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1606 Ramachandran restraints generated. 803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 50 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 640 MET cc_start: 0.7424 (ptm) cc_final: 0.7053 (ptm) REVERT: B 650 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7364 (tp) REVERT: B 740 TYR cc_start: 0.7836 (OUTLIER) cc_final: 0.7385 (t80) outliers start: 20 outliers final: 17 residues processed: 66 average time/residue: 0.1603 time to fit residues: 15.1542 Evaluate side-chains 66 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 47 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 740 TYR Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 785 LYS Chi-restraints excluded: chain B residue 817 PHE Chi-restraints excluded: chain B residue 837 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 3 optimal weight: 0.0060 chunk 45 optimal weight: 0.0170 overall best weight: 0.3234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.178069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.150993 restraints weight = 17675.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.151925 restraints weight = 13636.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.151695 restraints weight = 10958.425| |-----------------------------------------------------------------------------| r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6495 Z= 0.166 Angle : 0.718 10.537 8750 Z= 0.360 Chirality : 0.044 0.247 999 Planarity : 0.004 0.069 1119 Dihedral : 5.664 24.784 838 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.75 % Allowed : 13.95 % Favored : 85.31 % Rotamer: Outliers : 2.86 % Allowed : 22.86 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.28), residues: 803 helix: -0.72 (0.28), residues: 336 sheet: -2.34 (0.79), residues: 40 loop : -2.88 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 805 HIS 0.001 0.000 HIS B 216 PHE 0.035 0.002 PHE B 111 TYR 0.010 0.001 TYR B 206 ARG 0.004 0.001 ARG B 140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1473.78 seconds wall clock time: 27 minutes 51.46 seconds (1671.46 seconds total)