Starting phenix.real_space_refine on Sat Dec 28 20:50:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n3p_24143/12_2024/7n3p_24143.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n3p_24143/12_2024/7n3p_24143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n3p_24143/12_2024/7n3p_24143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n3p_24143/12_2024/7n3p_24143.map" model { file = "/net/cci-nas-00/data/ceres_data/7n3p_24143/12_2024/7n3p_24143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n3p_24143/12_2024/7n3p_24143.cif" } resolution = 3.65 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= 0.004 sd= 0.108 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: 5 Type Number sf(0) Gaussians P 259 5.49 5 S 12 5.16 5 C 4737 2.51 5 N 1634 2.21 5 O 2413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9055 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3561 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 16, 'TRANS': 437} Chain breaks: 3 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 14, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 90 Chain: "B" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 4883 Classifications: {'RNA': 229} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 14, 'rna3p_pur': 103, 'rna3p_pyr': 95} Link IDs: {'rna2p': 31, 'rna3p': 197} Chain breaks: 4 Chain: "C" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 399 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "D" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 212 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Time building chain proxies: 5.93, per 1000 atoms: 0.65 Number of scatterers: 9055 At special positions: 0 Unit cell: (100.8, 105, 124.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 259 15.00 O 2413 8.00 N 1634 7.00 C 4737 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: 2.29 Conformation dependent library (CDL) restraints added in 480.7 milliseconds 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 858 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 3 sheets defined 58.6% alpha, 11.9% beta 80 base pairs and 151 stacking pairs defined. Time for finding SS restraints: 4.15 Creating SS restraints... Processing helix chain 'A' and resid 13 through 25 removed outlier: 3.651A pdb=" N ARG A 17 " --> pdb=" O PHE A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 41 Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 57 through 68 Proline residue: A 65 - end of helix removed outlier: 3.896A pdb=" N THR A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 102 Processing helix chain 'A' and resid 321 through 338 removed outlier: 3.752A pdb=" N PHE A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 347 removed outlier: 3.785A pdb=" N LEU A 346 " --> pdb=" O SER A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 406 removed outlier: 3.700A pdb=" N GLU A 388 " --> pdb=" O GLU A 384 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A 390 " --> pdb=" O GLY A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 429 removed outlier: 3.656A pdb=" N THR A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'A' and resid 485 through 505 removed outlier: 3.696A pdb=" N ASN A 489 " --> pdb=" O TYR A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 538 Processing helix chain 'A' and resid 550 through 567 Processing helix chain 'A' and resid 570 through 585 removed outlier: 3.519A pdb=" N GLN A 574 " --> pdb=" O TYR A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 605 removed outlier: 3.969A pdb=" N LEU A 593 " --> pdb=" O SER A 589 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 603 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 637 Processing sheet with id=AA1, first strand: chain 'A' and resid 283 through 285 removed outlier: 6.389A pdb=" N LEU A 349 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASP A 378 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN A 351 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU A 371 " --> pdb=" O LEU A 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 292 through 295 Processing sheet with id=AA3, first strand: chain 'A' and resid 471 through 475 removed outlier: 3.665A pdb=" N ALA A 473 " --> pdb=" O VAL A 463 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N SER A 445 " --> pdb=" O ALA A 540 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N SER A 542 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 447 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N VAL A 544 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL A 449 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 607 " --> pdb=" O GLY A 541 " (cutoff:3.500A) 215 hydrogen bonds defined for protein. 630 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 203 hydrogen bonds 380 hydrogen bond angles 0 basepair planarities 80 basepair parallelities 151 stacking parallelities Total time for adding SS restraints: 4.42 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1456 1.33 - 1.45: 3855 1.45 - 1.57: 3931 1.57 - 1.69: 511 1.69 - 1.81: 18 Bond restraints: 9771 Sorted by residual: bond pdb=" O5' G B 57 " pdb=" C5' G B 57 " ideal model delta sigma weight residual 1.420 1.454 -0.034 1.50e-02 4.44e+03 5.25e+00 bond pdb=" P G B 224 " pdb=" OP2 G B 224 " ideal model delta sigma weight residual 1.485 1.524 -0.039 2.00e-02 2.50e+03 3.87e+00 bond pdb=" O5' G B 224 " pdb=" C5' G B 224 " ideal model delta sigma weight residual 1.420 1.449 -0.029 1.50e-02 4.44e+03 3.83e+00 bond pdb=" O5' G B 56 " pdb=" C5' G B 56 " ideal model delta sigma weight residual 1.424 1.453 -0.029 1.50e-02 4.44e+03 3.77e+00 bond pdb=" P G B 56 " pdb=" OP2 G B 56 " ideal model delta sigma weight residual 1.485 1.523 -0.038 2.00e-02 2.50e+03 3.69e+00 ... (remaining 9766 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 14131 1.64 - 3.28: 254 3.28 - 4.91: 58 4.91 - 6.55: 10 6.55 - 8.19: 6 Bond angle restraints: 14459 Sorted by residual: angle pdb=" O3' G B 56 " pdb=" C3' G B 56 " pdb=" C2' G B 56 " ideal model delta sigma weight residual 109.50 116.76 -7.26 1.50e+00 4.44e-01 2.34e+01 angle pdb=" O3' G B 189 " pdb=" C3' G B 189 " pdb=" C2' G B 189 " ideal model delta sigma weight residual 109.50 116.52 -7.02 1.50e+00 4.44e-01 2.19e+01 angle pdb=" C4' G B 56 " pdb=" C3' G B 56 " pdb=" O3' G B 56 " ideal model delta sigma weight residual 109.40 115.70 -6.30 1.50e+00 4.44e-01 1.76e+01 angle pdb=" C4' G B 189 " pdb=" C3' G B 189 " pdb=" O3' G B 189 " ideal model delta sigma weight residual 109.40 114.53 -5.13 1.50e+00 4.44e-01 1.17e+01 angle pdb=" N GLY A 569 " pdb=" CA GLY A 569 " pdb=" C GLY A 569 " ideal model delta sigma weight residual 113.18 120.19 -7.01 2.37e+00 1.78e-01 8.75e+00 ... (remaining 14454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.08: 5286 35.08 - 70.15: 688 70.15 - 105.23: 69 105.23 - 140.30: 2 140.30 - 175.38: 11 Dihedral angle restraints: 6056 sinusoidal: 4733 harmonic: 1323 Sorted by residual: dihedral pdb=" C4' G B 189 " pdb=" C3' G B 189 " pdb=" C2' G B 189 " pdb=" C1' G B 189 " ideal model delta sinusoidal sigma weight residual -35.00 32.64 -67.64 1 8.00e+00 1.56e-02 9.29e+01 dihedral pdb=" C5' G B 189 " pdb=" C4' G B 189 " pdb=" C3' G B 189 " pdb=" O3' G B 189 " ideal model delta sinusoidal sigma weight residual 147.00 79.79 67.21 1 8.00e+00 1.56e-02 9.19e+01 dihedral pdb=" O4' C B 196 " pdb=" C1' C B 196 " pdb=" N1 C B 196 " pdb=" C2 C B 196 " ideal model delta sinusoidal sigma weight residual 200.00 26.02 173.98 1 1.50e+01 4.44e-03 8.51e+01 ... (remaining 6053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1753 0.083 - 0.165: 54 0.165 - 0.248: 7 0.248 - 0.330: 3 0.330 - 0.413: 2 Chirality restraints: 1819 Sorted by residual: chirality pdb=" C3' G B 189 " pdb=" C4' G B 189 " pdb=" O3' G B 189 " pdb=" C2' G B 189 " both_signs ideal model delta sigma weight residual False -2.74 -2.33 -0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" C3' G B 56 " pdb=" C4' G B 56 " pdb=" O3' G B 56 " pdb=" C2' G B 56 " both_signs ideal model delta sigma weight residual False -2.74 -2.34 -0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" P G B 57 " pdb=" OP1 G B 57 " pdb=" OP2 G B 57 " pdb=" O5' G B 57 " both_signs ideal model delta sigma weight residual True 2.41 -2.72 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 1816 not shown) Planarity restraints: 887 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C B 96 " 0.025 2.00e-02 2.50e+03 1.54e-02 5.33e+00 pdb=" N1 C B 96 " -0.032 2.00e-02 2.50e+03 pdb=" C2 C B 96 " 0.004 2.00e-02 2.50e+03 pdb=" O2 C B 96 " -0.006 2.00e-02 2.50e+03 pdb=" N3 C B 96 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C B 96 " 0.020 2.00e-02 2.50e+03 pdb=" N4 C B 96 " -0.004 2.00e-02 2.50e+03 pdb=" C5 C B 96 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C B 96 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B 97 " 0.030 2.00e-02 2.50e+03 1.51e-02 5.16e+00 pdb=" N1 C B 97 " -0.030 2.00e-02 2.50e+03 pdb=" C2 C B 97 " -0.006 2.00e-02 2.50e+03 pdb=" O2 C B 97 " -0.004 2.00e-02 2.50e+03 pdb=" N3 C B 97 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C B 97 " 0.007 2.00e-02 2.50e+03 pdb=" N4 C B 97 " 0.006 2.00e-02 2.50e+03 pdb=" C5 C B 97 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C B 97 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 45 " 0.029 2.00e-02 2.50e+03 1.46e-02 4.81e+00 pdb=" N1 U B 45 " -0.030 2.00e-02 2.50e+03 pdb=" C2 U B 45 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U B 45 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U B 45 " 0.001 2.00e-02 2.50e+03 pdb=" C4 U B 45 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U B 45 " 0.008 2.00e-02 2.50e+03 pdb=" C5 U B 45 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U B 45 " -0.009 2.00e-02 2.50e+03 ... (remaining 884 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1338 2.76 - 3.29: 8146 3.29 - 3.83: 18195 3.83 - 4.36: 20224 4.36 - 4.90: 28501 Nonbonded interactions: 76404 Sorted by model distance: nonbonded pdb=" O6 G B 165 " pdb=" O4 U B 173 " model vdw 2.224 2.432 nonbonded pdb=" O2' G B 189 " pdb=" O5' A B 190 " model vdw 2.266 3.040 nonbonded pdb=" O2' A B 190 " pdb=" O4' A B 191 " model vdw 2.284 3.040 nonbonded pdb=" O2 U B 30 " pdb=" N1 G B 31 " model vdw 2.288 3.120 nonbonded pdb=" ND2 ASN A 379 " pdb=" OE1 GLN A 603 " model vdw 2.294 3.120 ... (remaining 76399 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.790 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 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 : 0.003 0.039 9771 Z= 0.153 Angle : 0.580 8.191 14459 Z= 0.308 Chirality : 0.037 0.413 1819 Planarity : 0.003 0.047 887 Dihedral : 24.550 175.377 5198 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: 1.68 (0.40), residues: 446 helix: 2.21 (0.33), residues: 244 sheet: -0.00 (0.61), residues: 67 loop : -0.27 (0.55), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 94 HIS 0.003 0.001 HIS A 353 PHE 0.012 0.002 PHE A 325 TYR 0.013 0.001 TYR A 570 ARG 0.017 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.561 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1859 time to fit residues: 16.7848 Evaluate side-chains 47 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 30.0000 chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 54 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN A 586 HIS ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9771 Z= 0.303 Angle : 0.668 8.011 14459 Z= 0.350 Chirality : 0.038 0.269 1819 Planarity : 0.005 0.065 887 Dihedral : 25.328 178.656 4362 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.43 % Allowed : 10.27 % Favored : 87.30 % 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: 1.30 (0.40), residues: 446 helix: 1.96 (0.33), residues: 246 sheet: -0.04 (0.63), residues: 69 loop : -0.71 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 48 HIS 0.004 0.001 HIS A 522 PHE 0.015 0.002 PHE A 347 TYR 0.012 0.002 TYR A 91 ARG 0.006 0.001 ARG A 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.538 Fit side-chains REVERT: A 81 MET cc_start: 0.7985 (tpp) cc_final: 0.7685 (tpp) REVERT: A 89 TYR cc_start: 0.7941 (m-10) cc_final: 0.7655 (m-10) REVERT: A 310 ASP cc_start: 0.8549 (p0) cc_final: 0.8235 (p0) outliers start: 9 outliers final: 4 residues processed: 53 average time/residue: 0.1523 time to fit residues: 12.8421 Evaluate side-chains 38 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 626 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 GLN A 496 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9771 Z= 0.306 Angle : 0.611 9.912 14459 Z= 0.322 Chirality : 0.036 0.227 1819 Planarity : 0.004 0.052 887 Dihedral : 25.352 178.950 4362 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.51 % Allowed : 11.62 % Favored : 84.86 % 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: 1.32 (0.40), residues: 446 helix: 2.01 (0.33), residues: 246 sheet: -0.09 (0.67), residues: 63 loop : -0.74 (0.51), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 588 HIS 0.005 0.001 HIS A 304 PHE 0.010 0.002 PHE A 325 TYR 0.011 0.002 TYR A 570 ARG 0.005 0.000 ARG A 17 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.840 Fit side-chains REVERT: A 89 TYR cc_start: 0.7981 (m-10) cc_final: 0.7629 (m-10) REVERT: A 273 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7974 (pp) REVERT: A 461 VAL cc_start: 0.9409 (t) cc_final: 0.9180 (p) outliers start: 13 outliers final: 7 residues processed: 57 average time/residue: 0.1729 time to fit residues: 15.4875 Evaluate side-chains 53 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 626 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 7 optimal weight: 0.1980 chunk 30 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 60 optimal weight: 50.0000 chunk 18 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9771 Z= 0.298 Angle : 0.608 8.723 14459 Z= 0.322 Chirality : 0.037 0.229 1819 Planarity : 0.004 0.050 887 Dihedral : 25.306 179.158 4362 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.78 % Allowed : 13.78 % Favored : 82.43 % 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: 1.24 (0.40), residues: 446 helix: 2.03 (0.33), residues: 242 sheet: -0.19 (0.64), residues: 64 loop : -0.83 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 588 HIS 0.003 0.001 HIS A 304 PHE 0.012 0.002 PHE A 325 TYR 0.014 0.002 TYR A 441 ARG 0.003 0.000 ARG A 17 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.602 Fit side-chains REVERT: A 89 TYR cc_start: 0.7992 (m-10) cc_final: 0.7740 (m-10) REVERT: A 273 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7999 (pp) REVERT: A 461 VAL cc_start: 0.9434 (t) cc_final: 0.9198 (p) outliers start: 14 outliers final: 8 residues processed: 60 average time/residue: 0.1662 time to fit residues: 15.2421 Evaluate side-chains 54 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 626 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 chunk 60 optimal weight: 50.0000 chunk 17 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9771 Z= 0.226 Angle : 0.571 9.527 14459 Z= 0.301 Chirality : 0.035 0.226 1819 Planarity : 0.004 0.046 887 Dihedral : 25.211 179.922 4362 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.51 % Allowed : 15.14 % Favored : 81.35 % 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: 1.35 (0.40), residues: 446 helix: 2.17 (0.33), residues: 242 sheet: -0.14 (0.65), residues: 64 loop : -0.88 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 588 HIS 0.003 0.001 HIS A 369 PHE 0.012 0.002 PHE A 305 TYR 0.012 0.001 TYR A 91 ARG 0.003 0.000 ARG A 17 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.514 Fit side-chains REVERT: A 89 TYR cc_start: 0.7960 (m-10) cc_final: 0.7662 (m-10) REVERT: A 273 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8001 (pp) REVERT: A 461 VAL cc_start: 0.9434 (t) cc_final: 0.9220 (p) outliers start: 13 outliers final: 9 residues processed: 59 average time/residue: 0.1665 time to fit residues: 15.1437 Evaluate side-chains 57 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 626 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 65 optimal weight: 20.0000 chunk 7 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9771 Z= 0.228 Angle : 0.574 9.494 14459 Z= 0.302 Chirality : 0.035 0.226 1819 Planarity : 0.004 0.039 887 Dihedral : 25.211 179.623 4362 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.78 % Allowed : 17.03 % Favored : 79.19 % 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: 1.39 (0.40), residues: 446 helix: 2.20 (0.33), residues: 242 sheet: -0.12 (0.66), residues: 64 loop : -0.85 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 588 HIS 0.003 0.001 HIS A 304 PHE 0.011 0.002 PHE A 325 TYR 0.011 0.001 TYR A 570 ARG 0.003 0.000 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.605 Fit side-chains REVERT: A 89 TYR cc_start: 0.7996 (m-10) cc_final: 0.7663 (m-10) REVERT: A 273 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8015 (pp) REVERT: A 290 ASP cc_start: 0.8053 (t0) cc_final: 0.7775 (t0) REVERT: A 461 VAL cc_start: 0.9439 (t) cc_final: 0.9224 (p) outliers start: 14 outliers final: 10 residues processed: 59 average time/residue: 0.1463 time to fit residues: 13.8305 Evaluate side-chains 58 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 626 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN A 446 HIS ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9771 Z= 0.151 Angle : 0.538 10.074 14459 Z= 0.282 Chirality : 0.033 0.222 1819 Planarity : 0.004 0.038 887 Dihedral : 25.108 178.768 4362 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.24 % Allowed : 19.19 % Favored : 77.57 % 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: 1.70 (0.41), residues: 446 helix: 2.46 (0.33), residues: 242 sheet: -0.07 (0.66), residues: 64 loop : -0.69 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 293 HIS 0.002 0.000 HIS A 304 PHE 0.009 0.001 PHE A 325 TYR 0.012 0.001 TYR A 570 ARG 0.003 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.592 Fit side-chains REVERT: A 89 TYR cc_start: 0.7886 (m-10) cc_final: 0.7553 (m-10) REVERT: A 273 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8102 (pp) REVERT: A 290 ASP cc_start: 0.8009 (t0) cc_final: 0.7570 (t0) REVERT: A 461 VAL cc_start: 0.9439 (t) cc_final: 0.9235 (p) REVERT: A 486 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7950 (pt0) outliers start: 12 outliers final: 8 residues processed: 60 average time/residue: 0.1561 time to fit residues: 14.5276 Evaluate side-chains 59 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 626 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 61 optimal weight: 30.0000 chunk 64 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 9771 Z= 0.452 Angle : 0.722 8.908 14459 Z= 0.374 Chirality : 0.042 0.233 1819 Planarity : 0.005 0.043 887 Dihedral : 25.289 178.547 4362 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.51 % Allowed : 21.08 % Favored : 75.41 % 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: 1.19 (0.40), residues: 446 helix: 2.03 (0.33), residues: 242 sheet: -0.10 (0.66), residues: 64 loop : -0.99 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 588 HIS 0.004 0.002 HIS A 586 PHE 0.014 0.002 PHE A 305 TYR 0.015 0.002 TYR A 441 ARG 0.004 0.001 ARG A 525 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.616 Fit side-chains REVERT: A 89 TYR cc_start: 0.8084 (m-10) cc_final: 0.7764 (m-10) REVERT: A 273 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8131 (pp) REVERT: A 290 ASP cc_start: 0.8110 (t0) cc_final: 0.7307 (t0) REVERT: A 461 VAL cc_start: 0.9461 (t) cc_final: 0.9241 (p) outliers start: 13 outliers final: 8 residues processed: 51 average time/residue: 0.1361 time to fit residues: 11.6580 Evaluate side-chains 49 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 626 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 59 optimal weight: 30.0000 chunk 62 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9771 Z= 0.153 Angle : 0.562 10.246 14459 Z= 0.292 Chirality : 0.033 0.231 1819 Planarity : 0.004 0.034 887 Dihedral : 25.130 179.780 4362 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.16 % Allowed : 22.16 % Favored : 75.68 % 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: 1.60 (0.41), residues: 446 helix: 2.40 (0.34), residues: 242 sheet: -0.06 (0.67), residues: 64 loop : -0.80 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 21 HIS 0.004 0.001 HIS A 304 PHE 0.013 0.002 PHE A 305 TYR 0.015 0.001 TYR A 91 ARG 0.003 0.000 ARG A 17 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.527 Fit side-chains REVERT: A 89 TYR cc_start: 0.7890 (m-10) cc_final: 0.7570 (m-10) REVERT: A 290 ASP cc_start: 0.8018 (t0) cc_final: 0.7752 (t0) outliers start: 8 outliers final: 6 residues processed: 54 average time/residue: 0.1428 time to fit residues: 12.3971 Evaluate side-chains 52 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 626 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 42 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 59 optimal weight: 30.0000 chunk 17 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9771 Z= 0.364 Angle : 0.678 11.034 14459 Z= 0.349 Chirality : 0.039 0.318 1819 Planarity : 0.004 0.038 887 Dihedral : 25.286 179.728 4362 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.89 % Allowed : 22.97 % Favored : 75.14 % 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: 1.27 (0.40), residues: 446 helix: 2.13 (0.33), residues: 242 sheet: -0.16 (0.67), residues: 64 loop : -0.97 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 588 HIS 0.004 0.001 HIS A 586 PHE 0.017 0.002 PHE A 305 TYR 0.014 0.002 TYR A 441 ARG 0.004 0.000 ARG A 525 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.618 Fit side-chains REVERT: A 89 TYR cc_start: 0.8057 (m-10) cc_final: 0.7781 (m-10) REVERT: A 290 ASP cc_start: 0.7923 (t0) cc_final: 0.7661 (t0) outliers start: 7 outliers final: 6 residues processed: 49 average time/residue: 0.1421 time to fit residues: 11.5383 Evaluate side-chains 48 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 626 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 0.8980 chunk 55 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.132593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.094715 restraints weight = 21087.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.097137 restraints weight = 11139.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.097170 restraints weight = 6728.813| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9771 Z= 0.191 Angle : 0.586 10.186 14459 Z= 0.302 Chirality : 0.035 0.230 1819 Planarity : 0.004 0.036 887 Dihedral : 25.183 179.757 4362 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.16 % Allowed : 22.43 % Favored : 75.41 % 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: 1.45 (0.41), residues: 446 helix: 2.28 (0.33), residues: 242 sheet: -0.22 (0.67), residues: 64 loop : -0.83 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 21 HIS 0.003 0.001 HIS A 304 PHE 0.012 0.002 PHE A 305 TYR 0.014 0.001 TYR A 91 ARG 0.002 0.000 ARG A 350 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1242.96 seconds wall clock time: 24 minutes 9.65 seconds (1449.65 seconds total)