Starting phenix.real_space_refine on Thu Nov 14 06:43:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teg_41185/11_2024/8teg_41185.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teg_41185/11_2024/8teg_41185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teg_41185/11_2024/8teg_41185.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teg_41185/11_2024/8teg_41185.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teg_41185/11_2024/8teg_41185.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teg_41185/11_2024/8teg_41185.cif" } resolution = 2.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 30 5.16 5 C 2926 2.51 5 N 716 2.21 5 O 846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 4518 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4247 Classifications: {'peptide': 539} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 503} Chain breaks: 2 Chain: "B" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 183 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 1, 'TRANS': 20} Chain: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 4.07, per 1000 atoms: 0.90 Number of scatterers: 4518 At special positions: 0 Unit cell: (73.87, 90.47, 84.66, 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 30 16.00 O 846 8.00 N 716 7.00 C 2926 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: 1.12 Conformation dependent library (CDL) restraints added in 565.9 milliseconds 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1036 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 3 sheets defined 76.6% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 8 through 20 removed outlier: 3.772A pdb=" N MET A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 31 removed outlier: 4.057A pdb=" N GLY A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 35 removed outlier: 3.776A pdb=" N ARG A 35 " --> pdb=" O ALA A 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 32 through 35' Processing helix chain 'A' and resid 36 through 62 removed outlier: 3.610A pdb=" N ILE A 49 " --> pdb=" O PHE A 45 " (cutoff:3.500A) Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 67 through 86 Processing helix chain 'A' and resid 96 through 112 removed outlier: 3.539A pdb=" N ALA A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 142 Processing helix chain 'A' and resid 143 through 151 removed outlier: 3.521A pdb=" N ILE A 147 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 148 " --> pdb=" O CYS A 145 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ASN A 149 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 178 removed outlier: 3.517A pdb=" N LEU A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 192 Processing helix chain 'A' and resid 193 through 219 removed outlier: 3.542A pdb=" N ARG A 219 " --> pdb=" O GLY A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 228 through 252 removed outlier: 6.235A pdb=" N VAL A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Proline residue: A 241 - end of helix Processing helix chain 'A' and resid 253 through 258 removed outlier: 4.572A pdb=" N GLY A 256 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 290 through 297 Processing helix chain 'A' and resid 297 through 320 removed outlier: 3.615A pdb=" N MET A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER A 313 " --> pdb=" O TYR A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 325 Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'A' and resid 359 through 368 Processing helix chain 'A' and resid 464 through 480 removed outlier: 3.924A pdb=" N VAL A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA A 479 " --> pdb=" O GLY A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 Processing helix chain 'A' and resid 488 through 503 removed outlier: 3.696A pdb=" N LEU A 492 " --> pdb=" O PRO A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 517 Processing helix chain 'A' and resid 519 through 521 No H-bonds generated for 'chain 'A' and resid 519 through 521' Processing helix chain 'A' and resid 522 through 528 removed outlier: 3.923A pdb=" N VAL A 526 " --> pdb=" O ARG A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 538 Processing helix chain 'A' and resid 539 through 561 Processing helix chain 'A' and resid 565 through 568 Processing helix chain 'A' and resid 569 through 584 removed outlier: 3.526A pdb=" N MET A 573 " --> pdb=" O MET A 569 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A 577 " --> pdb=" O MET A 573 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) Proline residue: A 579 - end of helix Processing helix chain 'A' and resid 584 through 589 removed outlier: 3.709A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 598 Processing helix chain 'A' and resid 609 through 614 Processing helix chain 'B' and resid 626 through 635 removed outlier: 3.731A pdb=" N GLU B 633 " --> pdb=" O GLU B 629 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 94 Processing sheet with id=AA2, first strand: chain 'A' and resid 369 through 371 Processing sheet with id=AA3, first strand: chain 'A' and resid 531 through 532 277 hydrogen bonds defined for protein. 795 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: 1.31 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.24: 568 1.24 - 1.38: 1174 1.38 - 1.53: 2133 1.53 - 1.67: 626 1.67 - 1.81: 52 Bond restraints: 4553 Sorted by residual: bond pdb=" CG PRO A 114 " pdb=" CD PRO A 114 " ideal model delta sigma weight residual 1.503 1.099 0.404 3.40e-02 8.65e+02 1.41e+02 bond pdb=" N PRO A 114 " pdb=" CA PRO A 114 " ideal model delta sigma weight residual 1.471 1.521 -0.050 1.32e-02 5.74e+03 1.42e+01 bond pdb=" N PRO A 114 " pdb=" CD PRO A 114 " ideal model delta sigma weight residual 1.473 1.515 -0.042 1.40e-02 5.10e+03 8.90e+00 bond pdb=" CA PRO A 114 " pdb=" CB PRO A 114 " ideal model delta sigma weight residual 1.534 1.509 0.025 1.43e-02 4.89e+03 3.05e+00 bond pdb=" N PHE A 5 " pdb=" CA PHE A 5 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 ... (remaining 4548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.01: 6179 5.01 - 10.02: 5 10.02 - 15.02: 0 15.02 - 20.03: 0 20.03 - 25.04: 2 Bond angle restraints: 6186 Sorted by residual: angle pdb=" N PRO A 114 " pdb=" CD PRO A 114 " pdb=" CG PRO A 114 " ideal model delta sigma weight residual 103.20 78.16 25.04 1.50e+00 4.44e-01 2.79e+02 angle pdb=" CA PRO A 114 " pdb=" CB PRO A 114 " pdb=" CG PRO A 114 " ideal model delta sigma weight residual 104.50 79.68 24.82 1.90e+00 2.77e-01 1.71e+02 angle pdb=" N PRO A 114 " pdb=" CA PRO A 114 " pdb=" CB PRO A 114 " ideal model delta sigma weight residual 103.30 97.17 6.13 1.12e+00 7.97e-01 3.00e+01 angle pdb=" CA PRO A 114 " pdb=" N PRO A 114 " pdb=" CD PRO A 114 " ideal model delta sigma weight residual 112.00 105.20 6.80 1.40e+00 5.10e-01 2.36e+01 angle pdb=" N LEU A 504 " pdb=" CA LEU A 504 " pdb=" C LEU A 504 " ideal model delta sigma weight residual 109.81 116.27 -6.46 2.21e+00 2.05e-01 8.54e+00 ... (remaining 6181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 2360 17.69 - 35.39: 245 35.39 - 53.08: 52 53.08 - 70.78: 9 70.78 - 88.47: 8 Dihedral angle restraints: 2674 sinusoidal: 1062 harmonic: 1612 Sorted by residual: dihedral pdb=" CA LYS A 590 " pdb=" C LYS A 590 " pdb=" N GLY A 591 " pdb=" CA GLY A 591 " ideal model delta harmonic sigma weight residual 180.00 157.04 22.96 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" N PRO A 114 " pdb=" CG PRO A 114 " pdb=" CD PRO A 114 " pdb=" CB PRO A 114 " ideal model delta sinusoidal sigma weight residual 30.00 81.50 -51.50 1 1.50e+01 4.44e-03 1.61e+01 dihedral pdb=" CA LEU A 504 " pdb=" C LEU A 504 " pdb=" N PRO A 505 " pdb=" CA PRO A 505 " ideal model delta harmonic sigma weight residual -180.00 -160.62 -19.38 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 2671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 444 0.030 - 0.060: 173 0.060 - 0.090: 51 0.090 - 0.120: 23 0.120 - 0.150: 7 Chirality restraints: 698 Sorted by residual: chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CA PRO A 505 " pdb=" N PRO A 505 " pdb=" C PRO A 505 " pdb=" CB PRO A 505 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA PRO A 564 " pdb=" N PRO A 564 " pdb=" C PRO A 564 " pdb=" CB PRO A 564 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 695 not shown) Planarity restraints: 769 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 580 " 0.006 2.00e-02 2.50e+03 1.17e-02 1.37e+00 pdb=" C VAL A 580 " -0.020 2.00e-02 2.50e+03 pdb=" O VAL A 580 " 0.008 2.00e-02 2.50e+03 pdb=" N ARG A 581 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 97 " -0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO A 98 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 98 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 98 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 253 " -0.016 5.00e-02 4.00e+02 2.47e-02 9.76e-01 pdb=" N PRO A 254 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 254 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 254 " -0.014 5.00e-02 4.00e+02 ... (remaining 766 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 226 2.73 - 3.27: 4804 3.27 - 3.81: 7945 3.81 - 4.36: 9877 4.36 - 4.90: 15723 Nonbonded interactions: 38575 Sorted by model distance: nonbonded pdb=" O ALA A 144 " pdb=" OH TYR A 309 " model vdw 2.185 3.040 nonbonded pdb=" OD1 ASP A 25 " pdb=" NZ LYS A 328 " model vdw 2.317 3.120 nonbonded pdb=" N GLU A 323 " pdb=" OE1 GLU A 323 " model vdw 2.414 3.120 nonbonded pdb=" OD2 ASP A 335 " pdb=" O HOH A 801 " model vdw 2.419 3.040 nonbonded pdb=" O LYS A 260 " pdb=" O HOH A 802 " model vdw 2.442 3.040 ... (remaining 38570 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 3.700 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.730 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 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 : 0.007 0.404 4553 Z= 0.348 Angle : 0.742 25.041 6186 Z= 0.415 Chirality : 0.039 0.150 698 Planarity : 0.004 0.027 769 Dihedral : 15.683 88.472 1638 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.05 % Allowed : 9.28 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.36), residues: 553 helix: 1.36 (0.27), residues: 384 sheet: -1.48 (1.36), residues: 10 loop : 1.33 (0.50), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 PHE 0.012 0.001 PHE A 534 TYR 0.013 0.001 TYR A 495 ARG 0.004 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.576 Fit side-chains REVERT: A 114 PRO cc_start: 0.7985 (Cg_exo) cc_final: 0.7612 (Cg_exo) REVERT: B 629 GLU cc_start: 0.8387 (tt0) cc_final: 0.8178 (tt0) outliers start: 5 outliers final: 3 residues processed: 69 average time/residue: 1.9456 time to fit residues: 138.1844 Evaluate side-chains 67 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 462 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 0.0670 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.0070 chunk 32 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.0711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4553 Z= 0.148 Angle : 0.553 10.184 6186 Z= 0.283 Chirality : 0.040 0.143 698 Planarity : 0.004 0.029 769 Dihedral : 4.856 37.653 612 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.05 % Allowed : 9.07 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 2.25 (0.36), residues: 553 helix: 1.81 (0.27), residues: 377 sheet: -2.44 (1.28), residues: 10 loop : 1.25 (0.50), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 PHE 0.020 0.001 PHE A 298 TYR 0.007 0.001 TYR A 495 ARG 0.003 0.000 ARG B 637 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.588 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 73 average time/residue: 1.7305 time to fit residues: 130.1630 Evaluate side-chains 67 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 463 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 0.0670 chunk 15 optimal weight: 4.9990 chunk 41 optimal weight: 0.0870 chunk 34 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 54 optimal weight: 0.4980 chunk 44 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 17 optimal weight: 0.0070 chunk 40 optimal weight: 0.9990 overall best weight: 0.2914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4553 Z= 0.133 Angle : 0.493 7.311 6186 Z= 0.253 Chirality : 0.039 0.136 698 Planarity : 0.004 0.030 769 Dihedral : 4.398 39.958 605 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.48 % Allowed : 10.13 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 2.39 (0.36), residues: 553 helix: 1.90 (0.27), residues: 379 sheet: -2.62 (1.30), residues: 10 loop : 1.38 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 247 HIS 0.002 0.001 HIS A 312 PHE 0.015 0.001 PHE A 298 TYR 0.008 0.001 TYR A 495 ARG 0.003 0.000 ARG B 637 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.524 Fit side-chains REVERT: A 617 GLU cc_start: 0.6093 (OUTLIER) cc_final: 0.5699 (tt0) outliers start: 7 outliers final: 2 residues processed: 69 average time/residue: 1.5869 time to fit residues: 113.0594 Evaluate side-chains 64 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 617 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4553 Z= 0.169 Angle : 0.539 7.525 6186 Z= 0.279 Chirality : 0.041 0.144 698 Planarity : 0.004 0.034 769 Dihedral : 4.506 41.903 605 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.48 % Allowed : 9.70 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 2.22 (0.36), residues: 553 helix: 1.76 (0.27), residues: 378 sheet: -2.76 (1.34), residues: 10 loop : 1.34 (0.50), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 131 HIS 0.003 0.001 HIS A 312 PHE 0.016 0.001 PHE A 534 TYR 0.011 0.001 TYR A 495 ARG 0.003 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.534 Fit side-chains REVERT: A 617 GLU cc_start: 0.6074 (OUTLIER) cc_final: 0.5648 (tt0) outliers start: 7 outliers final: 3 residues processed: 69 average time/residue: 1.5953 time to fit residues: 113.5966 Evaluate side-chains 65 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 617 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 27 optimal weight: 0.0270 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 0.0020 chunk 17 optimal weight: 0.9980 overall best weight: 0.7848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4553 Z= 0.176 Angle : 0.551 7.664 6186 Z= 0.286 Chirality : 0.042 0.148 698 Planarity : 0.004 0.035 769 Dihedral : 4.591 43.324 605 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.69 % Allowed : 9.70 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 2.09 (0.36), residues: 553 helix: 1.66 (0.27), residues: 378 sheet: -2.87 (1.34), residues: 10 loop : 1.30 (0.50), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 PHE 0.016 0.001 PHE A 534 TYR 0.011 0.001 TYR A 495 ARG 0.003 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.515 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 69 average time/residue: 1.6325 time to fit residues: 116.1372 Evaluate side-chains 64 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 463 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 51 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4553 Z= 0.163 Angle : 0.538 7.615 6186 Z= 0.278 Chirality : 0.041 0.145 698 Planarity : 0.004 0.034 769 Dihedral : 4.556 43.379 605 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.05 % Allowed : 10.34 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 2.15 (0.36), residues: 553 helix: 1.70 (0.27), residues: 378 sheet: -2.90 (1.34), residues: 10 loop : 1.34 (0.50), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 PHE 0.016 0.001 PHE A 298 TYR 0.010 0.001 TYR A 495 ARG 0.003 0.000 ARG B 637 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.463 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 67 average time/residue: 1.5811 time to fit residues: 109.3438 Evaluate side-chains 65 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 463 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4553 Z= 0.171 Angle : 0.547 7.650 6186 Z= 0.283 Chirality : 0.041 0.147 698 Planarity : 0.004 0.035 769 Dihedral : 4.579 43.745 605 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.27 % Allowed : 9.92 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 2.11 (0.36), residues: 553 helix: 1.68 (0.27), residues: 378 sheet: -2.91 (1.34), residues: 10 loop : 1.31 (0.50), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 PHE 0.016 0.001 PHE A 298 TYR 0.011 0.001 TYR A 495 ARG 0.003 0.000 ARG B 637 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.525 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 66 average time/residue: 1.6350 time to fit residues: 111.3336 Evaluate side-chains 66 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 463 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4553 Z= 0.230 Angle : 0.611 7.792 6186 Z= 0.320 Chirality : 0.045 0.161 698 Planarity : 0.005 0.037 769 Dihedral : 4.771 45.573 605 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.48 % Allowed : 10.13 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.36), residues: 553 helix: 1.41 (0.27), residues: 384 sheet: -2.82 (1.37), residues: 10 loop : 1.31 (0.50), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 131 HIS 0.003 0.001 HIS A 312 PHE 0.017 0.002 PHE A 534 TYR 0.014 0.002 TYR A 495 ARG 0.004 0.001 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.536 Fit side-chains REVERT: A 257 ASP cc_start: 0.7297 (OUTLIER) cc_final: 0.6938 (m-30) REVERT: A 502 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8314 (mt-10) outliers start: 7 outliers final: 3 residues processed: 68 average time/residue: 1.6524 time to fit residues: 116.0250 Evaluate side-chains 68 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 502 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 31 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4553 Z= 0.166 Angle : 0.542 7.720 6186 Z= 0.281 Chirality : 0.041 0.148 698 Planarity : 0.004 0.034 769 Dihedral : 4.612 43.232 605 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.05 % Allowed : 10.34 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 2.04 (0.36), residues: 553 helix: 1.58 (0.27), residues: 384 sheet: -2.88 (1.36), residues: 10 loop : 1.41 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 PHE 0.017 0.001 PHE A 298 TYR 0.010 0.001 TYR A 293 ARG 0.004 0.000 ARG B 637 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.554 Fit side-chains REVERT: A 502 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8270 (mt-10) outliers start: 5 outliers final: 3 residues processed: 67 average time/residue: 1.6679 time to fit residues: 115.1619 Evaluate side-chains 67 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 502 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 34 optimal weight: 0.1980 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4553 Z= 0.190 Angle : 0.574 7.665 6186 Z= 0.298 Chirality : 0.043 0.152 698 Planarity : 0.005 0.036 769 Dihedral : 4.659 43.811 605 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.84 % Allowed : 10.55 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.36), residues: 553 helix: 1.50 (0.27), residues: 384 sheet: -2.83 (1.38), residues: 10 loop : 1.37 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 247 HIS 0.003 0.001 HIS A 312 PHE 0.018 0.002 PHE A 298 TYR 0.012 0.001 TYR A 495 ARG 0.003 0.000 ARG B 637 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.553 Fit side-chains REVERT: A 502 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8294 (mt-10) outliers start: 4 outliers final: 3 residues processed: 65 average time/residue: 1.6639 time to fit residues: 111.5218 Evaluate side-chains 66 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 502 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.123998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.099868 restraints weight = 3952.781| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.09 r_work: 0.2938 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4553 Z= 0.180 Angle : 0.567 7.691 6186 Z= 0.293 Chirality : 0.042 0.150 698 Planarity : 0.004 0.035 769 Dihedral : 4.657 43.551 605 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.05 % Allowed : 10.55 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.36), residues: 553 helix: 1.51 (0.27), residues: 384 sheet: -2.84 (1.38), residues: 10 loop : 1.41 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 PHE 0.017 0.001 PHE A 298 TYR 0.011 0.001 TYR A 495 ARG 0.004 0.000 ARG B 637 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2585.23 seconds wall clock time: 46 minutes 37.13 seconds (2797.13 seconds total)