Starting phenix.real_space_refine on Fri Dec 8 01:04:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9b_15275/12_2023/8a9b_15275.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9b_15275/12_2023/8a9b_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_15275/12_2023/8a9b_15275.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9b_15275/12_2023/8a9b_15275.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9b_15275/12_2023/8a9b_15275.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9b_15275/12_2023/8a9b_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 4.07, per 1000 atoms: 0.64 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: 2.09 Conformation dependent library (CDL) restraints added in 1.1 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: 0.66 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: 1.84 Time building geometry restraints manager: 2.31 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: 0.820 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: 3.800 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 20.150 Find NCS groups from input model: 0.170 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.850 ------------------------------------------------------------------------------- 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 : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1887 time to fit residues: 18.9903 Evaluate side-chains 45 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.673 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9791 ------------------------------------------------------------------------------- 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: 4.9990 chunk 32 optimal weight: 0.9980 chunk 62 optimal weight: 0.0170 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 72 optimal weight: 0.1980 overall best weight: 0.6422 ------------------------------------------------------------------------------- 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 849 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5837 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6495 Z= 0.230 Angle : 0.763 10.291 8750 Z= 0.393 Chirality : 0.048 0.503 999 Planarity : 0.004 0.054 1119 Dihedral : 6.228 36.259 838 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 20.75 Ramachandran Plot: Outliers : 0.87 % Allowed : 14.32 % Favored : 84.81 % Rotamer: Outliers : 1.00 % Allowed : 9.57 % Favored : 89.43 % 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: -3.01 (0.28), residues: 803 helix: -0.84 (0.28), residues: 329 sheet: -2.32 (0.85), residues: 44 loop : -3.03 (0.27), residues: 430 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 0.017 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 64 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 61 average time/residue: 0.1637 time to fit residues: 14.6322 Evaluate side-chains 50 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.710 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1506 time to fit residues: 1.5961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 49 optimal weight: 0.0000 chunk 20 optimal weight: 0.4980 chunk 72 optimal weight: 0.7980 chunk 78 optimal weight: 0.3980 chunk 64 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 58 optimal weight: 0.0980 chunk 71 optimal weight: 4.9990 overall best weight: 0.3384 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5770 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6495 Z= 0.172 Angle : 0.723 9.981 8750 Z= 0.367 Chirality : 0.046 0.507 999 Planarity : 0.004 0.056 1119 Dihedral : 5.966 34.433 838 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.87 % Allowed : 13.45 % Favored : 85.68 % Rotamer: Outliers : 0.86 % Allowed : 13.71 % Favored : 85.43 % 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: -2.83 (0.29), residues: 803 helix: -0.75 (0.28), residues: 338 sheet: -2.51 (0.86), residues: 42 loop : -2.87 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 805 HIS 0.001 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 56 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 56 average time/residue: 0.1374 time to fit residues: 12.1205 Evaluate side-chains 46 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.746 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0703 time to fit residues: 1.5722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 0.4980 chunk 37 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.0670 chunk 20 optimal weight: 1.9990 chunk 64 optimal weight: 0.1980 overall best weight: 0.5120 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5819 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6495 Z= 0.192 Angle : 0.728 12.656 8750 Z= 0.367 Chirality : 0.044 0.231 999 Planarity : 0.004 0.059 1119 Dihedral : 5.806 24.898 838 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.75 % Allowed : 13.45 % Favored : 85.80 % Rotamer: Outliers : 1.57 % Allowed : 16.14 % Favored : 82.29 % 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: -2.91 (0.29), residues: 803 helix: -0.72 (0.28), residues: 337 sheet: -2.89 (0.67), residues: 58 loop : -2.93 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 805 HIS 0.002 0.001 HIS B 216 PHE 0.023 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 57 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 46 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 54 average time/residue: 0.1427 time to fit residues: 12.0671 Evaluate side-chains 43 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.755 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0603 time to fit residues: 1.4028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 57 optimal weight: 0.2980 chunk 31 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.5872 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6495 Z= 0.205 Angle : 0.718 9.797 8750 Z= 0.363 Chirality : 0.045 0.231 999 Planarity : 0.004 0.062 1119 Dihedral : 5.823 24.451 838 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.75 % Allowed : 14.07 % Favored : 85.18 % Rotamer: Outliers : 1.14 % Allowed : 17.86 % Favored : 81.00 % 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: -2.90 (0.29), residues: 803 helix: -0.64 (0.29), residues: 330 sheet: -3.06 (0.70), residues: 52 loop : -2.95 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 805 HIS 0.001 0.001 HIS B 216 PHE 0.037 0.002 PHE B 111 TYR 0.012 0.001 TYR B 751 ARG 0.005 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 52 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 51 average time/residue: 0.1395 time to fit residues: 11.0394 Evaluate side-chains 47 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.657 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0735 time to fit residues: 1.5818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.0980 chunk 15 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 35 optimal weight: 7.9990 chunk 6 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.0870 chunk 74 optimal weight: 0.9980 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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: 0.5830 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6495 Z= 0.179 Angle : 0.704 9.870 8750 Z= 0.353 Chirality : 0.044 0.229 999 Planarity : 0.004 0.063 1119 Dihedral : 5.660 23.720 838 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.75 % Allowed : 13.57 % Favored : 85.68 % Rotamer: Outliers : 1.29 % Allowed : 18.71 % Favored : 80.00 % 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: -2.85 (0.29), residues: 803 helix: -0.75 (0.28), residues: 338 sheet: -2.93 (0.72), residues: 52 loop : -2.83 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 805 HIS 0.001 0.001 HIS B 216 PHE 0.028 0.002 PHE B 111 TYR 0.009 0.001 TYR B 187 ARG 0.004 0.000 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 62 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 61 average time/residue: 0.1395 time to fit residues: 13.1255 Evaluate side-chains 47 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.771 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0713 time to fit residues: 2.0082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 48 optimal weight: 0.0970 chunk 47 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5898 moved from start: 0.2814 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= 0.226 Angle : 0.758 12.003 8750 Z= 0.377 Chirality : 0.047 0.416 999 Planarity : 0.004 0.064 1119 Dihedral : 5.831 22.843 838 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.75 % Allowed : 15.19 % Favored : 84.06 % Rotamer: Outliers : 0.57 % Allowed : 20.43 % Favored : 79.00 % 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: -2.98 (0.28), residues: 803 helix: -0.86 (0.28), residues: 335 sheet: -2.98 (0.82), residues: 34 loop : -2.92 (0.28), residues: 434 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 0.024 0.002 PHE B 111 TYR 0.012 0.001 TYR B 751 ARG 0.005 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 49 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 49 average time/residue: 0.1405 time to fit residues: 10.7453 Evaluate side-chains 45 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.735 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0649 time to fit residues: 1.3031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 7 optimal weight: 5.9990 chunk 60 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5878 moved from start: 0.2980 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= 0.196 Angle : 0.722 10.039 8750 Z= 0.364 Chirality : 0.045 0.248 999 Planarity : 0.004 0.065 1119 Dihedral : 5.785 22.354 838 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.75 % Allowed : 14.07 % Favored : 85.18 % Rotamer: Outliers : 0.71 % Allowed : 21.00 % Favored : 78.29 % 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: -2.95 (0.28), residues: 803 helix: -0.85 (0.28), residues: 335 sheet: -2.93 (0.82), residues: 34 loop : -2.90 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 805 HIS 0.001 0.001 HIS B 216 PHE 0.032 0.002 PHE B 359 TYR 0.010 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 53 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 51 average time/residue: 0.1340 time to fit residues: 10.7253 Evaluate side-chains 48 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.701 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0716 time to fit residues: 1.3882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 0.0470 chunk 73 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 0.4980 chunk 46 optimal weight: 0.6980 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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: 0.5883 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6495 Z= 0.188 Angle : 0.711 8.910 8750 Z= 0.359 Chirality : 0.045 0.233 999 Planarity : 0.004 0.064 1119 Dihedral : 5.742 22.449 838 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.75 % Allowed : 14.20 % Favored : 85.06 % Rotamer: Outliers : 0.86 % Allowed : 21.43 % Favored : 77.71 % 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: -2.93 (0.28), residues: 803 helix: -0.86 (0.28), residues: 335 sheet: -2.46 (0.80), residues: 40 loop : -2.90 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 805 HIS 0.001 0.000 HIS B 216 PHE 0.027 0.002 PHE B 854 TYR 0.010 0.001 TYR B 751 ARG 0.004 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 54 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 54 average time/residue: 0.1416 time to fit residues: 12.0089 Evaluate side-chains 48 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.733 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0633 time to fit residues: 1.1784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0030 chunk 79 optimal weight: 0.2980 chunk 73 optimal weight: 0.0000 chunk 63 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 50 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.2594 ------------------------------------------------------------------------------- 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 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5799 moved from start: 0.3389 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= 0.156 Angle : 0.687 9.244 8750 Z= 0.347 Chirality : 0.044 0.227 999 Planarity : 0.004 0.064 1119 Dihedral : 5.593 21.312 838 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.75 % Allowed : 13.70 % Favored : 85.55 % Rotamer: Outliers : 0.43 % Allowed : 22.57 % Favored : 77.00 % 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: -2.83 (0.28), residues: 803 helix: -0.80 (0.28), residues: 336 sheet: -2.21 (0.91), residues: 31 loop : -2.85 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 805 HIS 0.001 0.000 HIS B 216 PHE 0.028 0.002 PHE B 854 TYR 0.008 0.001 TYR B 187 ARG 0.003 0.000 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 52 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 50 average time/residue: 0.1403 time to fit residues: 10.9586 Evaluate side-chains 46 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.752 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0634 time to fit residues: 1.1704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.0040 chunk 63 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.177341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.148737 restraints weight = 17979.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.148717 restraints weight = 15012.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.148760 restraints weight = 14105.356| |-----------------------------------------------------------------------------| r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6495 Z= 0.223 Angle : 0.730 9.142 8750 Z= 0.371 Chirality : 0.045 0.222 999 Planarity : 0.004 0.063 1119 Dihedral : 5.797 21.463 838 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 20.75 Ramachandran Plot: Outliers : 0.75 % Allowed : 14.82 % Favored : 84.43 % Rotamer: Outliers : 0.43 % Allowed : 22.86 % Favored : 76.71 % 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: -2.95 (0.28), residues: 803 helix: -0.91 (0.28), residues: 335 sheet: -2.61 (1.07), residues: 20 loop : -2.89 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 121 HIS 0.001 0.001 HIS B 580 PHE 0.032 0.002 PHE B 359 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: 1469.90 seconds wall clock time: 28 minutes 24.71 seconds (1704.71 seconds total)