Starting phenix.real_space_refine on Fri Dec 27 11:47:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bzy_16345/12_2024/8bzy_16345.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bzy_16345/12_2024/8bzy_16345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bzy_16345/12_2024/8bzy_16345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bzy_16345/12_2024/8bzy_16345.map" model { file = "/net/cci-nas-00/data/ceres_data/8bzy_16345/12_2024/8bzy_16345.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bzy_16345/12_2024/8bzy_16345.cif" } resolution = 3.24 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 31 5.16 5 C 2817 2.51 5 N 702 2.21 5 O 759 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4311 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3300 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 9, 'TRANS': 419} Chain breaks: 2 Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 942 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 69 Unusual residues: {'PLC': 1, 'SZU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 3.95, per 1000 atoms: 0.92 Number of scatterers: 4311 At special positions: 0 Unit cell: (89.838, 87.885, 69.006, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 31 16.00 P 1 15.00 F 1 9.00 O 759 8.00 N 702 7.00 C 2817 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 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: 1.37 Conformation dependent library (CDL) restraints added in 542.8 milliseconds 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1004 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 3 sheets defined 73.8% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 18 through 22 removed outlier: 3.563A pdb=" N LEU A 21 " --> pdb=" O ALA A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 54 Processing helix chain 'A' and resid 57 through 86 removed outlier: 3.808A pdb=" N THR A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ALA A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ILE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 Processing helix chain 'A' and resid 116 through 122 Processing helix chain 'A' and resid 125 through 164 removed outlier: 4.430A pdb=" N LEU A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 199 Proline residue: A 189 - end of helix Processing helix chain 'A' and resid 200 through 230 removed outlier: 3.730A pdb=" N VAL A 221 " --> pdb=" O CYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.647A pdb=" N ALA A 234 " --> pdb=" O PRO A 231 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 235 " --> pdb=" O ALA A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 235' Processing helix chain 'A' and resid 288 through 304 Processing helix chain 'A' and resid 308 through 317 Processing helix chain 'A' and resid 330 through 336 Processing helix chain 'A' and resid 338 through 367 removed outlier: 3.958A pdb=" N ARG A 365 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 366 " --> pdb=" O TRP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 393 Processing helix chain 'A' and resid 451 through 484 removed outlier: 3.521A pdb=" N VAL A 455 " --> pdb=" O PRO A 451 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER A 471 " --> pdb=" O ILE A 467 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE A 472 " --> pdb=" O GLY A 468 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 514 Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 519 through 546 Processing helix chain 'B' and resid 61 through 65 removed outlier: 3.513A pdb=" N LYS B 65 " --> pdb=" O ASP B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.735A pdb=" N THR B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.119A pdb=" N GLY B 10 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N SER B 120 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL B 12 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU B 33 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.119A pdb=" N GLY B 10 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N SER B 120 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL B 12 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N TYR B 108 " --> pdb=" O ASP B 100 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY B 102 " --> pdb=" O TRP B 106 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) 347 hydrogen bonds defined for protein. 1017 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: 1.28 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 654 1.31 - 1.43: 1236 1.43 - 1.56: 2462 1.56 - 1.68: 2 1.68 - 1.81: 52 Bond restraints: 4406 Sorted by residual: bond pdb=" C1 SZU A 602 " pdb=" N1 SZU A 602 " ideal model delta sigma weight residual 1.347 1.450 -0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" C8 SZU A 602 " pdb=" N6 SZU A 602 " ideal model delta sigma weight residual 1.396 1.319 0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C1 SZU A 602 " pdb=" O1 SZU A 602 " ideal model delta sigma weight residual 1.233 1.184 0.049 2.00e-02 2.50e+03 6.11e+00 bond pdb=" C1 SZU A 602 " pdb=" C8 SZU A 602 " ideal model delta sigma weight residual 1.476 1.524 -0.048 2.00e-02 2.50e+03 5.65e+00 bond pdb=" C15 SZU A 602 " pdb=" N4 SZU A 602 " ideal model delta sigma weight residual 1.370 1.323 0.047 2.00e-02 2.50e+03 5.52e+00 ... (remaining 4401 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 5910 1.99 - 3.97: 69 3.97 - 5.96: 6 5.96 - 7.94: 1 7.94 - 9.93: 2 Bond angle restraints: 5988 Sorted by residual: angle pdb=" O3P PLC A 601 " pdb=" P PLC A 601 " pdb=" O4P PLC A 601 " ideal model delta sigma weight residual 93.62 103.55 -9.93 3.00e+00 1.11e-01 1.10e+01 angle pdb=" CA LEU A 503 " pdb=" CB LEU A 503 " pdb=" CG LEU A 503 " ideal model delta sigma weight residual 116.30 106.94 9.36 3.50e+00 8.16e-02 7.15e+00 angle pdb=" C11 SZU A 602 " pdb=" C10 SZU A 602 " pdb=" O2 SZU A 602 " ideal model delta sigma weight residual 117.54 125.10 -7.56 3.00e+00 1.11e-01 6.36e+00 angle pdb=" C GLY A 199 " pdb=" N SER A 200 " pdb=" CA SER A 200 " ideal model delta sigma weight residual 121.80 127.47 -5.67 2.44e+00 1.68e-01 5.41e+00 angle pdb=" N ALA B 104 " pdb=" CA ALA B 104 " pdb=" C ALA B 104 " ideal model delta sigma weight residual 110.97 113.44 -2.47 1.09e+00 8.42e-01 5.14e+00 ... (remaining 5983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.48: 2499 28.48 - 56.96: 50 56.96 - 85.43: 0 85.43 - 113.91: 2 113.91 - 142.39: 2 Dihedral angle restraints: 2553 sinusoidal: 979 harmonic: 1574 Sorted by residual: dihedral pdb=" C13 SZU A 602 " pdb=" C14 SZU A 602 " pdb=" C15 SZU A 602 " pdb=" N4 SZU A 602 " ideal model delta sinusoidal sigma weight residual 286.49 144.10 142.39 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C13 SZU A 602 " pdb=" C14 SZU A 602 " pdb=" C15 SZU A 602 " pdb=" N5 SZU A 602 " ideal model delta sinusoidal sigma weight residual 105.00 -35.33 140.33 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" O2 PLC A 601 " pdb=" C1 PLC A 601 " pdb=" C2 PLC A 601 " pdb=" O3P PLC A 601 " ideal model delta sinusoidal sigma weight residual -55.71 54.64 -110.35 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 2550 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 387 0.025 - 0.050: 193 0.050 - 0.075: 79 0.075 - 0.100: 29 0.100 - 0.125: 9 Chirality restraints: 697 Sorted by residual: chirality pdb=" CA VAL B 93 " pdb=" N VAL B 93 " pdb=" C VAL B 93 " pdb=" CB VAL B 93 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" C2 PLC A 601 " pdb=" C1 PLC A 601 " pdb=" C3 PLC A 601 " pdb=" O2 PLC A 601 " both_signs ideal model delta sigma weight residual False -2.31 -2.44 0.12 2.00e-01 2.50e+01 3.73e-01 chirality pdb=" CA VAL B 79 " pdb=" N VAL B 79 " pdb=" C VAL B 79 " pdb=" CB VAL B 79 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.92e-01 ... (remaining 694 not shown) Planarity restraints: 725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 155 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C GLN A 155 " 0.033 2.00e-02 2.50e+03 pdb=" O GLN A 155 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG A 156 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 525 " -0.009 2.00e-02 2.50e+03 1.73e-02 2.98e+00 pdb=" C LEU A 525 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU A 525 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE A 526 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 527 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.56e+00 pdb=" C SER A 527 " 0.028 2.00e-02 2.50e+03 pdb=" O SER A 527 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL A 528 " -0.009 2.00e-02 2.50e+03 ... (remaining 722 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1229 2.82 - 3.34: 4397 3.34 - 3.86: 7399 3.86 - 4.38: 8083 4.38 - 4.90: 14661 Nonbonded interactions: 35769 Sorted by model distance: nonbonded pdb=" O ALA B 52 " pdb=" NH1 ARG B 72 " model vdw 2.297 3.120 nonbonded pdb=" OG SER A 390 " pdb=" O SER A 454 " model vdw 2.339 3.040 nonbonded pdb=" O ASN A 86 " pdb=" NZ LYS A 236 " model vdw 2.361 3.120 nonbonded pdb=" O VAL B 29 " pdb=" NH2 ARG B 72 " model vdw 2.398 3.120 nonbonded pdb=" O LEU A 60 " pdb=" OH TYR A 133 " model vdw 2.407 3.040 ... (remaining 35764 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: 0.000 Normalize map: mean=0, sd=1: 3.540 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.610 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 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 : 0.005 0.103 4406 Z= 0.286 Angle : 0.553 9.930 5988 Z= 0.274 Chirality : 0.037 0.125 697 Planarity : 0.004 0.026 725 Dihedral : 12.927 142.389 1546 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.42 % Allowed : 4.63 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.37), residues: 541 helix: 2.49 (0.27), residues: 366 sheet: 0.15 (0.76), residues: 40 loop : -1.43 (0.54), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 470 HIS 0.002 0.001 HIS A 43 PHE 0.013 0.001 PHE A 295 TYR 0.008 0.001 TYR A 64 ARG 0.002 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.434 Fit side-chains REVERT: B 103 MET cc_start: 0.9205 (ptt) cc_final: 0.8682 (ptp) outliers start: 11 outliers final: 8 residues processed: 47 average time/residue: 0.2383 time to fit residues: 14.5999 Evaluate side-chains 45 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 56 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN A 228 GLN B 13 GLN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4406 Z= 0.211 Angle : 0.465 8.488 5988 Z= 0.246 Chirality : 0.037 0.119 697 Planarity : 0.003 0.029 725 Dihedral : 10.593 86.193 652 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.86 % Allowed : 6.83 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.36), residues: 541 helix: 2.84 (0.25), residues: 367 sheet: 0.21 (0.77), residues: 40 loop : -1.34 (0.54), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.002 0.001 HIS A 43 PHE 0.012 0.001 PHE A 295 TYR 0.018 0.001 TYR B 60 ARG 0.006 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.456 Fit side-chains REVERT: B 103 MET cc_start: 0.9205 (ptt) cc_final: 0.8804 (ptp) outliers start: 13 outliers final: 8 residues processed: 52 average time/residue: 0.1874 time to fit residues: 12.3827 Evaluate side-chains 48 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 56 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4406 Z= 0.253 Angle : 0.490 9.481 5988 Z= 0.254 Chirality : 0.037 0.119 697 Planarity : 0.003 0.030 725 Dihedral : 9.096 61.571 650 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.42 % Allowed : 8.81 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.36), residues: 541 helix: 2.84 (0.26), residues: 366 sheet: 0.05 (0.79), residues: 40 loop : -1.33 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 224 HIS 0.003 0.001 HIS A 507 PHE 0.012 0.001 PHE A 295 TYR 0.016 0.001 TYR B 60 ARG 0.006 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.451 Fit side-chains REVERT: B 103 MET cc_start: 0.9189 (ptt) cc_final: 0.8838 (ptp) outliers start: 11 outliers final: 9 residues processed: 47 average time/residue: 0.1745 time to fit residues: 10.6510 Evaluate side-chains 47 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 56 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 52 optimal weight: 0.2980 chunk 46 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 GLN B 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4406 Z= 0.187 Angle : 0.439 7.875 5988 Z= 0.230 Chirality : 0.036 0.117 697 Planarity : 0.003 0.031 725 Dihedral : 8.258 58.471 649 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.64 % Allowed : 9.47 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.36), residues: 541 helix: 3.08 (0.26), residues: 366 sheet: 0.14 (0.80), residues: 40 loop : -1.30 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 224 HIS 0.002 0.001 HIS A 32 PHE 0.011 0.001 PHE A 295 TYR 0.018 0.001 TYR B 60 ARG 0.008 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.451 Fit side-chains REVERT: B 72 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.6818 (ptm160) REVERT: B 103 MET cc_start: 0.9140 (ptt) cc_final: 0.8866 (ptp) outliers start: 12 outliers final: 8 residues processed: 47 average time/residue: 0.2258 time to fit residues: 13.2834 Evaluate side-chains 47 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 72 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 44 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4406 Z= 0.219 Angle : 0.453 8.234 5988 Z= 0.238 Chirality : 0.036 0.117 697 Planarity : 0.003 0.031 725 Dihedral : 8.131 55.825 647 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.52 % Allowed : 9.47 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.36), residues: 541 helix: 3.05 (0.25), residues: 366 sheet: 0.15 (0.80), residues: 40 loop : -1.27 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 470 HIS 0.002 0.001 HIS A 507 PHE 0.011 0.001 PHE A 295 TYR 0.014 0.001 TYR B 60 ARG 0.008 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.490 Fit side-chains REVERT: B 38 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.6819 (ptm160) REVERT: B 72 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.6741 (ptm160) REVERT: B 103 MET cc_start: 0.9157 (ptt) cc_final: 0.8868 (ptp) outliers start: 16 outliers final: 9 residues processed: 51 average time/residue: 0.2101 time to fit residues: 13.4567 Evaluate side-chains 49 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 72 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 24 optimal weight: 0.0870 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4406 Z= 0.210 Angle : 0.462 8.756 5988 Z= 0.238 Chirality : 0.036 0.117 697 Planarity : 0.003 0.031 725 Dihedral : 8.005 55.063 647 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.30 % Allowed : 10.35 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.36), residues: 541 helix: 3.08 (0.25), residues: 366 sheet: 0.20 (0.80), residues: 40 loop : -1.24 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 470 HIS 0.002 0.001 HIS A 32 PHE 0.011 0.001 PHE A 295 TYR 0.013 0.001 TYR B 60 ARG 0.008 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.466 Fit side-chains REVERT: A 312 MET cc_start: 0.6813 (mmm) cc_final: 0.6376 (mmm) REVERT: B 38 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6808 (ptm160) REVERT: B 72 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.6758 (ptm160) REVERT: B 103 MET cc_start: 0.9116 (ptt) cc_final: 0.8855 (ptp) outliers start: 15 outliers final: 9 residues processed: 51 average time/residue: 0.2038 time to fit residues: 12.9676 Evaluate side-chains 49 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 72 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 0.2980 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 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4406 Z= 0.229 Angle : 0.470 8.798 5988 Z= 0.244 Chirality : 0.036 0.115 697 Planarity : 0.003 0.031 725 Dihedral : 8.014 55.269 647 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.30 % Allowed : 10.35 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.36), residues: 541 helix: 3.02 (0.26), residues: 366 sheet: 0.33 (0.81), residues: 40 loop : -1.23 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 470 HIS 0.002 0.001 HIS A 507 PHE 0.011 0.001 PHE A 295 TYR 0.011 0.001 TYR B 60 ARG 0.008 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.453 Fit side-chains REVERT: A 228 GLN cc_start: 0.7223 (tp40) cc_final: 0.6966 (tp40) REVERT: B 38 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6818 (ptm160) REVERT: B 72 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.6738 (ptm160) REVERT: B 103 MET cc_start: 0.9098 (ptt) cc_final: 0.8850 (ptp) outliers start: 15 outliers final: 9 residues processed: 51 average time/residue: 0.2115 time to fit residues: 13.5153 Evaluate side-chains 50 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 72 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.7980 chunk 25 optimal weight: 0.1980 chunk 4 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4406 Z= 0.195 Angle : 0.463 8.290 5988 Z= 0.239 Chirality : 0.036 0.116 697 Planarity : 0.003 0.031 725 Dihedral : 7.826 56.648 647 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.64 % Allowed : 11.01 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.36), residues: 541 helix: 3.09 (0.26), residues: 366 sheet: 0.39 (0.81), residues: 40 loop : -1.21 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 106 HIS 0.002 0.001 HIS A 32 PHE 0.011 0.001 PHE A 295 TYR 0.012 0.001 TYR B 60 ARG 0.009 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.416 Fit side-chains REVERT: A 228 GLN cc_start: 0.7196 (tp40) cc_final: 0.6929 (tp40) REVERT: B 38 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.6825 (ptm160) REVERT: B 72 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.6762 (ptm160) REVERT: B 103 MET cc_start: 0.9044 (ptt) cc_final: 0.8839 (ptp) outliers start: 12 outliers final: 9 residues processed: 48 average time/residue: 0.2191 time to fit residues: 13.0541 Evaluate side-chains 48 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 72 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.0070 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4406 Z= 0.201 Angle : 0.459 8.266 5988 Z= 0.239 Chirality : 0.036 0.115 697 Planarity : 0.003 0.031 725 Dihedral : 7.775 58.542 647 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.42 % Allowed : 11.01 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.36), residues: 541 helix: 3.06 (0.26), residues: 367 sheet: 0.41 (0.81), residues: 40 loop : -1.23 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 470 HIS 0.002 0.001 HIS A 32 PHE 0.011 0.001 PHE A 295 TYR 0.012 0.001 TYR B 60 ARG 0.009 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.503 Fit side-chains REVERT: A 312 MET cc_start: 0.6775 (mmm) cc_final: 0.6440 (mmm) REVERT: B 38 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6819 (ptm160) REVERT: B 72 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.6751 (ptm160) REVERT: B 103 MET cc_start: 0.9048 (ptt) cc_final: 0.8827 (ptp) outliers start: 11 outliers final: 9 residues processed: 47 average time/residue: 0.2230 time to fit residues: 13.0432 Evaluate side-chains 48 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 72 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 39 optimal weight: 0.0030 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4406 Z= 0.187 Angle : 0.453 8.091 5988 Z= 0.236 Chirality : 0.036 0.115 697 Planarity : 0.003 0.031 725 Dihedral : 7.678 59.886 647 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.64 % Allowed : 11.23 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.36), residues: 541 helix: 3.11 (0.26), residues: 367 sheet: 0.44 (0.81), residues: 40 loop : -1.19 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 224 HIS 0.002 0.001 HIS A 32 PHE 0.011 0.001 PHE A 295 TYR 0.012 0.001 TYR B 60 ARG 0.009 0.001 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.547 Fit side-chains REVERT: A 312 MET cc_start: 0.6732 (mmm) cc_final: 0.6392 (mmm) REVERT: B 38 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6809 (ptm160) REVERT: B 72 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.6787 (ptm160) REVERT: B 103 MET cc_start: 0.9036 (ptt) cc_final: 0.8823 (ptp) outliers start: 12 outliers final: 9 residues processed: 48 average time/residue: 0.2217 time to fit residues: 13.4996 Evaluate side-chains 48 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 72 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 30 optimal weight: 0.0050 chunk 49 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.134817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.103538 restraints weight = 4538.422| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.94 r_work: 0.2950 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4406 Z= 0.190 Angle : 0.460 8.178 5988 Z= 0.238 Chirality : 0.036 0.115 697 Planarity : 0.003 0.031 725 Dihedral : 7.637 58.639 647 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.64 % Allowed : 11.23 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.36), residues: 541 helix: 3.11 (0.26), residues: 367 sheet: 0.45 (0.81), residues: 40 loop : -1.20 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 224 HIS 0.002 0.001 HIS A 32 PHE 0.011 0.001 PHE A 295 TYR 0.012 0.001 TYR B 60 ARG 0.008 0.001 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1352.74 seconds wall clock time: 25 minutes 30.45 seconds (1530.45 seconds total)