Starting phenix.real_space_refine on Tue Sep 24 00:43:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9b_15275/09_2024/8a9b_15275.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9b_15275/09_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_15275/09_2024/8a9b_15275.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9b_15275/09_2024/8a9b_15275.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9b_15275/09_2024/8a9b_15275.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9b_15275/09_2024/8a9b_15275.cif" } 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. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 4.31, per 1000 atoms: 0.67 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 913.0 milliseconds 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: 1.68 Time building geometry restraints manager: 1.83 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: 0.00 - 3.81: 8685 3.81 - 7.62: 56 7.62 - 11.44: 7 11.44 - 15.25: 0 15.25 - 19.06: 2 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 3.040 nonbonded pdb=" OG SER B 311 " pdb=" O LEU B 484 " model vdw 2.153 3.040 nonbonded pdb=" OE1 GLU B 306 " pdb=" NZ LYS B 575 " model vdw 2.190 3.120 nonbonded pdb=" OE1 GLU B 758 " pdb=" OG SER B 838 " model vdw 2.211 3.040 nonbonded pdb=" OG1 THR B 768 " pdb=" O PHE B 823 " model vdw 2.220 3.040 ... (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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.470 Find NCS groups from input model: 0.050 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.920 ------------------------------------------------------------------------------- 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 : 0.756 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: 0.1898 time to fit residues: 18.9952 Evaluate side-chains 46 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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: 0.9980 chunk 33 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 62 optimal weight: 0.0020 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 46 optimal weight: 0.3980 chunk 72 optimal weight: 0.4980 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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: 0.5774 moved from start: 0.1367 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= 0.207 Angle : 0.766 10.383 8750 Z= 0.396 Chirality : 0.048 0.508 999 Planarity : 0.004 0.052 1119 Dihedral : 6.166 35.651 838 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.87 % Allowed : 13.57 % Favored : 85.55 % Rotamer: Outliers : 0.86 % Allowed : 8.86 % Favored : 90.29 % 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: -3.09 (0.28), residues: 803 helix: -0.98 (0.27), residues: 336 sheet: -2.46 (0.78), residues: 49 loop : -3.01 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 121 HIS 0.002 0.001 HIS B 266 PHE 0.028 0.002 PHE B 854 TYR 0.018 0.001 TYR B 187 ARG 0.002 0.001 ARG B 331 *********************** 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: 6 poor density : 59 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 294 MET cc_start: 0.5570 (mtt) cc_final: 0.5090 (mmp) REVERT: B 447 LEU cc_start: 0.7286 (mm) cc_final: 0.7016 (mm) REVERT: B 640 MET cc_start: 0.7459 (ptm) cc_final: 0.7036 (ptm) outliers start: 6 outliers final: 2 residues processed: 63 average time/residue: 0.1596 time to fit residues: 14.4302 Evaluate side-chains 51 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 LEU 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: 4.9990 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 0.0060 chunk 72 optimal weight: 0.4980 chunk 78 optimal weight: 0.1980 chunk 64 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 71 optimal weight: 0.0270 overall best weight: 0.2454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 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: 0.5678 moved from start: 0.1930 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= 0.163 Angle : 0.725 9.817 8750 Z= 0.369 Chirality : 0.046 0.492 999 Planarity : 0.004 0.054 1119 Dihedral : 5.935 34.440 838 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.75 % Allowed : 12.70 % Favored : 86.55 % Rotamer: Outliers : 1.00 % Allowed : 13.29 % Favored : 85.71 % 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: -2.86 (0.28), residues: 803 helix: -0.75 (0.28), residues: 330 sheet: -2.43 (0.80), residues: 51 loop : -2.88 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 805 HIS 0.001 0.000 HIS B 216 PHE 0.027 0.002 PHE B 854 TYR 0.014 0.001 TYR B 187 ARG 0.002 0.000 ARG B 832 *********************** 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 63 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 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 447 LEU cc_start: 0.7285 (mm) cc_final: 0.7008 (mm) REVERT: B 640 MET cc_start: 0.7029 (ptm) cc_final: 0.6609 (ptm) outliers start: 7 outliers final: 6 residues processed: 61 average time/residue: 0.1723 time to fit residues: 14.9501 Evaluate side-chains 51 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 759 ILE Chi-restraints excluded: chain B residue 766 VAL 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: 1.9990 chunk 37 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 0.0470 chunk 20 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5914 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6495 Z= 0.270 Angle : 0.796 12.511 8750 Z= 0.402 Chirality : 0.047 0.251 999 Planarity : 0.004 0.061 1119 Dihedral : 6.019 25.161 838 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.62 % Allowed : 13.57 % Favored : 85.80 % Rotamer: Outliers : 2.43 % Allowed : 15.57 % Favored : 82.00 % 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: -2.95 (0.28), residues: 803 helix: -0.79 (0.28), residues: 326 sheet: -2.55 (0.84), residues: 42 loop : -2.95 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 121 HIS 0.002 0.001 HIS B 216 PHE 0.023 0.002 PHE B 111 TYR 0.016 0.002 TYR B 751 ARG 0.004 0.001 ARG B 850 *********************** 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 65 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 48 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 447 LEU cc_start: 0.7511 (mm) cc_final: 0.6753 (tp) REVERT: B 465 MET cc_start: 0.4695 (OUTLIER) cc_final: 0.3708 (mtm) REVERT: B 669 ASP cc_start: 0.6134 (m-30) cc_final: 0.5900 (p0) outliers start: 17 outliers final: 10 residues processed: 62 average time/residue: 0.1602 time to fit residues: 14.2757 Evaluate side-chains 54 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 616 VAL 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: 1.9990 chunk 1 optimal weight: 9.9990 chunk 57 optimal weight: 0.0980 chunk 31 optimal weight: 0.9990 chunk 65 optimal weight: 0.2980 chunk 53 optimal weight: 0.0170 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 69 optimal weight: 0.0980 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 overall best weight: 0.2418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.5758 moved from start: 0.2424 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= 0.166 Angle : 0.697 9.522 8750 Z= 0.350 Chirality : 0.044 0.227 999 Planarity : 0.004 0.063 1119 Dihedral : 5.698 24.227 838 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.62 % Allowed : 12.20 % Favored : 87.17 % Rotamer: Outliers : 1.86 % Allowed : 18.14 % 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: -2.79 (0.29), residues: 803 helix: -0.72 (0.28), residues: 333 sheet: -2.49 (0.76), residues: 51 loop : -2.82 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 805 HIS 0.001 0.000 HIS B 216 PHE 0.024 0.002 PHE B 854 TYR 0.009 0.001 TYR B 187 ARG 0.002 0.000 ARG B 400 *********************** 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 63 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 50 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 447 LEU cc_start: 0.6924 (mm) cc_final: 0.6340 (tp) REVERT: B 640 MET cc_start: 0.7275 (ptm) cc_final: 0.6919 (ptm) outliers start: 13 outliers final: 9 residues processed: 61 average time/residue: 0.1504 time to fit residues: 13.4473 Evaluate side-chains 50 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 785 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.0970 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 64 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** B 863 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5862 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6495 Z= 0.211 Angle : 0.742 10.063 8750 Z= 0.372 Chirality : 0.045 0.233 999 Planarity : 0.004 0.060 1119 Dihedral : 5.756 23.449 838 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.62 % Allowed : 13.33 % Favored : 86.05 % Rotamer: Outliers : 1.86 % Allowed : 19.57 % Favored : 78.57 % 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: -2.82 (0.28), residues: 803 helix: -0.73 (0.28), residues: 327 sheet: -1.99 (0.97), residues: 31 loop : -2.89 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 805 HIS 0.001 0.001 HIS B 216 PHE 0.024 0.002 PHE B 854 TYR 0.013 0.001 TYR B 751 ARG 0.002 0.001 ARG B 708 *********************** 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 59 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 46 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 216 HIS cc_start: 0.2060 (OUTLIER) cc_final: 0.1710 (m90) REVERT: B 447 LEU cc_start: 0.7253 (mm) cc_final: 0.7028 (mm) REVERT: B 669 ASP cc_start: 0.6134 (m-30) cc_final: 0.5871 (p0) outliers start: 13 outliers final: 11 residues processed: 56 average time/residue: 0.1426 time to fit residues: 12.0760 Evaluate side-chains 54 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 42 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain B residue 412 VAL 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 616 VAL Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 785 LYS 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: 3.9990 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 77 optimal weight: 0.0170 chunk 48 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.5844 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6495 Z= 0.197 Angle : 0.715 9.421 8750 Z= 0.360 Chirality : 0.044 0.222 999 Planarity : 0.004 0.064 1119 Dihedral : 5.760 22.962 838 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.50 % Allowed : 13.57 % Favored : 85.93 % Rotamer: Outliers : 2.71 % Allowed : 20.14 % Favored : 77.14 % 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: -2.83 (0.28), residues: 803 helix: -0.80 (0.28), residues: 332 sheet: -1.99 (0.95), residues: 32 loop : -2.87 (0.28), residues: 439 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 0.031 0.002 PHE B 359 TYR 0.011 0.001 TYR B 751 ARG 0.002 0.000 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 64 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 45 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 216 HIS cc_start: 0.1971 (OUTLIER) cc_final: 0.1670 (m90) REVERT: B 447 LEU cc_start: 0.7237 (mm) cc_final: 0.6994 (mm) REVERT: B 669 ASP cc_start: 0.6169 (m-30) cc_final: 0.5857 (p0) outliers start: 19 outliers final: 15 residues processed: 61 average time/residue: 0.1620 time to fit residues: 14.2899 Evaluate side-chains 59 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 43 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 412 VAL 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 616 VAL 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6052 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 6495 Z= 0.313 Angle : 0.823 10.893 8750 Z= 0.419 Chirality : 0.048 0.237 999 Planarity : 0.005 0.062 1119 Dihedral : 6.359 24.418 838 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 21.77 Ramachandran Plot: Outliers : 0.50 % Allowed : 15.32 % Favored : 84.18 % Rotamer: Outliers : 2.71 % Allowed : 20.43 % Favored : 76.86 % 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: -3.23 (0.27), residues: 803 helix: -1.08 (0.27), residues: 332 sheet: -2.25 (0.91), residues: 32 loop : -3.13 (0.26), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 121 HIS 0.003 0.001 HIS B 216 PHE 0.026 0.002 PHE B 498 TYR 0.014 0.002 TYR B 751 ARG 0.003 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 69 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 50 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 159 PHE cc_start: 0.3464 (m-80) cc_final: 0.3033 (m-80) REVERT: B 447 LEU cc_start: 0.7319 (mm) cc_final: 0.7048 (mm) REVERT: B 740 TYR cc_start: 0.8127 (OUTLIER) cc_final: 0.7582 (t80) outliers start: 19 outliers final: 15 residues processed: 66 average time/residue: 0.1415 time to fit residues: 13.8585 Evaluate side-chains 60 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 44 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 436 VAL 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 616 VAL 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 0.2980 chunk 73 optimal weight: 0.0070 chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 67 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN B 277 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 moved from start: 0.3496 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= 0.194 Angle : 0.737 10.531 8750 Z= 0.371 Chirality : 0.045 0.230 999 Planarity : 0.004 0.064 1119 Dihedral : 6.021 23.815 838 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.50 % Allowed : 13.82 % Favored : 85.68 % Rotamer: Outliers : 2.57 % Allowed : 21.00 % Favored : 76.43 % 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: -3.10 (0.28), residues: 803 helix: -1.02 (0.27), residues: 333 sheet: -2.13 (0.90), residues: 32 loop : -3.02 (0.27), residues: 438 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 0.030 0.002 PHE B 854 TYR 0.013 0.001 TYR B 623 ARG 0.002 0.000 ARG B 708 *********************** 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 63 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 45 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 ILE cc_start: 0.6365 (mt) cc_final: 0.5961 (mt) REVERT: B 447 LEU cc_start: 0.7148 (mm) cc_final: 0.6893 (mm) REVERT: B 633 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8085 (mmmm) REVERT: B 740 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7460 (t80) outliers start: 18 outliers final: 15 residues processed: 60 average time/residue: 0.1473 time to fit residues: 13.0383 Evaluate side-chains 60 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 43 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 412 VAL 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 616 VAL Chi-restraints excluded: chain B residue 633 LYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 79 optimal weight: 0.2980 chunk 73 optimal weight: 0.4980 chunk 63 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 50 optimal weight: 0.0770 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5919 moved from start: 0.3763 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= 0.199 Angle : 0.732 11.683 8750 Z= 0.366 Chirality : 0.045 0.233 999 Planarity : 0.004 0.064 1119 Dihedral : 5.789 21.888 838 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.50 % Allowed : 14.20 % Favored : 85.31 % Rotamer: Outliers : 2.29 % Allowed : 21.71 % Favored : 76.00 % 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: -3.02 (0.28), residues: 803 helix: -0.96 (0.27), residues: 334 sheet: -2.10 (0.91), residues: 32 loop : -2.97 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 121 HIS 0.002 0.001 HIS B 580 PHE 0.030 0.002 PHE B 854 TYR 0.013 0.001 TYR B 206 ARG 0.002 0.001 ARG B 850 ********************** 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 59 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 43 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 ILE cc_start: 0.6278 (mt) cc_final: 0.5858 (mt) REVERT: B 640 MET cc_start: 0.7428 (ptm) cc_final: 0.7141 (ptm) REVERT: B 740 TYR cc_start: 0.7739 (OUTLIER) cc_final: 0.7174 (t80) outliers start: 16 outliers final: 15 residues processed: 56 average time/residue: 0.1644 time to fit residues: 13.3054 Evaluate side-chains 58 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 42 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 412 VAL 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 616 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.2980 chunk 9 optimal weight: 0.0000 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 8 optimal weight: 0.0870 chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 849 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.178111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.150390 restraints weight = 17382.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.150948 restraints weight = 14606.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.150683 restraints weight = 12524.664| |-----------------------------------------------------------------------------| r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.3951 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= 0.188 Angle : 0.724 10.081 8750 Z= 0.362 Chirality : 0.045 0.236 999 Planarity : 0.004 0.065 1119 Dihedral : 5.741 21.616 838 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.50 % Allowed : 13.57 % Favored : 85.93 % Rotamer: Outliers : 2.43 % Allowed : 21.57 % Favored : 76.00 % 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: -2.92 (0.28), residues: 803 helix: -0.83 (0.28), residues: 333 sheet: -1.99 (0.89), residues: 32 loop : -2.96 (0.27), residues: 438 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 0.034 0.002 PHE B 854 TYR 0.011 0.001 TYR B 751 ARG 0.003 0.001 ARG B 331 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1475.89 seconds wall clock time: 27 minutes 24.63 seconds (1644.63 seconds total)