Starting phenix.real_space_refine on Thu Feb 13 15:30:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n3p_24143/02_2025/7n3p_24143.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n3p_24143/02_2025/7n3p_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_24143/02_2025/7n3p_24143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n3p_24143/02_2025/7n3p_24143.map" model { file = "/net/cci-nas-00/data/ceres_data/7n3p_24143/02_2025/7n3p_24143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n3p_24143/02_2025/7n3p_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.98, per 1000 atoms: 0.66 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: 2.19 Conformation dependent library (CDL) restraints added in 452.8 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: 3.81 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: 4.27 Time building geometry restraints manager: 2.58 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 26.660 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.630 ------------------------------------------------------------------------------- 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 : 0.568 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1997 time to fit residues: 18.3383 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 : 0.557 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.136296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.095813 restraints weight = 21659.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.098807 restraints weight = 8737.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.100565 restraints weight = 5725.747| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 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 : 0.579 Fit side-chains REVERT: A 81 MET cc_start: 0.7964 (tpp) cc_final: 0.7660 (tpp) REVERT: A 89 TYR cc_start: 0.7945 (m-10) cc_final: 0.7652 (m-10) REVERT: A 310 ASP cc_start: 0.8552 (p0) cc_final: 0.8240 (p0) outliers start: 9 outliers final: 4 residues processed: 53 average time/residue: 0.1534 time to fit residues: 12.6936 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 : 0.566 ------------------------------------------------------------------------------- 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 43 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.133007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.093284 restraints weight = 21217.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.096004 restraints weight = 8904.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.097668 restraints weight = 5908.680| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9771 Z= 0.322 Angle : 0.623 9.832 14459 Z= 0.329 Chirality : 0.037 0.227 1819 Planarity : 0.004 0.053 887 Dihedral : 25.382 178.772 4362 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.92 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: 1.26 (0.40), residues: 446 helix: 1.96 (0.33), residues: 246 sheet: -0.11 (0.67), residues: 63 loop : -0.75 (0.51), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 588 HIS 0.005 0.001 HIS A 304 PHE 0.010 0.002 PHE A 281 TYR 0.010 0.002 TYR A 570 ARG 0.004 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 60 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.592 Fit side-chains REVERT: A 89 TYR cc_start: 0.7975 (m-10) cc_final: 0.7655 (m-10) REVERT: A 273 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7958 (pp) REVERT: A 461 VAL cc_start: 0.9405 (t) cc_final: 0.9182 (p) outliers start: 13 outliers final: 7 residues processed: 56 average time/residue: 0.1741 time to fit residues: 14.7486 Evaluate side-chains 51 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 7 optimal weight: 0.3980 chunk 46 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.134406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.094869 restraints weight = 21074.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.097723 restraints weight = 8693.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.099393 restraints weight = 5714.875| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9771 Z= 0.209 Angle : 0.556 9.406 14459 Z= 0.295 Chirality : 0.034 0.226 1819 Planarity : 0.004 0.048 887 Dihedral : 25.235 179.844 4362 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.24 % Allowed : 13.24 % Favored : 83.51 % 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: 1.50 (0.40), residues: 446 helix: 2.25 (0.34), residues: 242 sheet: -0.10 (0.65), residues: 64 loop : -0.71 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 588 HIS 0.003 0.001 HIS A 304 PHE 0.010 0.002 PHE A 325 TYR 0.010 0.001 TYR A 570 ARG 0.004 0.000 ARG A 380 *********************** 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: 12 poor density : 51 time to evaluate : 0.545 Fit side-chains REVERT: A 89 TYR cc_start: 0.7947 (m-10) cc_final: 0.7676 (m-10) REVERT: A 273 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7954 (pp) REVERT: A 461 VAL cc_start: 0.9429 (t) cc_final: 0.9208 (p) REVERT: A 486 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7978 (pt0) outliers start: 12 outliers final: 7 residues processed: 59 average time/residue: 0.1609 time to fit residues: 14.5713 Evaluate side-chains 55 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 526 LEU 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 53 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 27 optimal weight: 0.4980 chunk 26 optimal weight: 5.9990 chunk 54 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 chunk 17 optimal weight: 0.3980 chunk 4 optimal weight: 0.0020 chunk 49 optimal weight: 6.9990 overall best weight: 2.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.131931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.094203 restraints weight = 21033.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.095962 restraints weight = 10375.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.096161 restraints weight = 6392.037| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9771 Z= 0.263 Angle : 0.588 9.407 14459 Z= 0.310 Chirality : 0.036 0.228 1819 Planarity : 0.004 0.041 887 Dihedral : 25.216 179.275 4362 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.05 % Allowed : 13.51 % 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: 1.35 (0.40), residues: 446 helix: 2.17 (0.33), residues: 242 sheet: -0.10 (0.66), residues: 64 loop : -0.88 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 588 HIS 0.003 0.001 HIS A 304 PHE 0.011 0.002 PHE A 325 TYR 0.012 0.002 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 63 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.641 Fit side-chains REVERT: A 89 TYR cc_start: 0.7936 (m-10) cc_final: 0.7604 (m-10) REVERT: A 273 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7981 (pp) outliers start: 15 outliers final: 8 residues processed: 59 average time/residue: 0.1582 time to fit residues: 14.4985 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 : 0.608 ------------------------------------------------------------------------------- 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 585 VAL 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 40 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 59 optimal weight: 30.0000 chunk 48 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN A 446 HIS ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.135836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.097056 restraints weight = 21009.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.099854 restraints weight = 8830.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.101644 restraints weight = 5844.825| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3037 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= 0.133 Angle : 0.527 10.513 14459 Z= 0.276 Chirality : 0.032 0.224 1819 Planarity : 0.004 0.035 887 Dihedral : 25.010 179.559 4362 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.97 % Allowed : 16.22 % Favored : 80.81 % 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: 1.75 (0.41), residues: 446 helix: 2.48 (0.34), residues: 242 sheet: 0.12 (0.66), residues: 64 loop : -0.71 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 21 HIS 0.002 0.000 HIS A 304 PHE 0.009 0.001 PHE A 325 TYR 0.011 0.001 TYR A 570 ARG 0.004 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 65 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.579 Fit side-chains REVERT: A 89 TYR cc_start: 0.7855 (m-10) cc_final: 0.7509 (m-10) REVERT: A 273 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8015 (pp) REVERT: A 290 ASP cc_start: 0.7958 (t0) cc_final: 0.7716 (t0) outliers start: 11 outliers final: 5 residues processed: 61 average time/residue: 0.1466 time to fit residues: 14.1507 Evaluate side-chains 56 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 303 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 26 optimal weight: 0.4980 chunk 23 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 59 optimal weight: 30.0000 chunk 69 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.127535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.087051 restraints weight = 21294.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.089684 restraints weight = 9391.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.091282 restraints weight = 6351.436| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 9771 Z= 0.461 Angle : 0.741 8.777 14459 Z= 0.383 Chirality : 0.042 0.239 1819 Planarity : 0.005 0.040 887 Dihedral : 25.341 178.126 4362 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.24 % Allowed : 17.84 % Favored : 78.92 % 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: 1.04 (0.40), residues: 446 helix: 1.89 (0.32), residues: 246 sheet: -0.29 (0.67), residues: 64 loop : -1.04 (0.50), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 356 HIS 0.007 0.002 HIS A 304 PHE 0.012 0.002 PHE A 305 TYR 0.013 0.003 TYR A 441 ARG 0.003 0.001 ARG A 525 *********************** 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 54 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.549 Fit side-chains REVERT: A 89 TYR cc_start: 0.8051 (m-10) cc_final: 0.7697 (m-10) REVERT: A 273 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8056 (pp) REVERT: A 290 ASP cc_start: 0.8033 (t0) cc_final: 0.7781 (t0) REVERT: A 310 ASP cc_start: 0.8405 (p0) cc_final: 0.8172 (p0) outliers start: 12 outliers final: 8 residues processed: 49 average time/residue: 0.1365 time to fit residues: 11.1705 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 : 0.615 ------------------------------------------------------------------------------- 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 291 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 628 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 28 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 60 optimal weight: 50.0000 chunk 43 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 0 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3958 r_free = 0.3958 target = 0.134256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.095172 restraints weight = 21390.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.097993 restraints weight = 8928.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.099768 restraints weight = 5872.236| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9771 Z= 0.138 Angle : 0.548 10.451 14459 Z= 0.286 Chirality : 0.033 0.237 1819 Planarity : 0.004 0.033 887 Dihedral : 25.089 179.380 4362 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.70 % Allowed : 18.38 % Favored : 78.92 % 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: 1.53 (0.41), residues: 446 helix: 2.45 (0.34), residues: 242 sheet: -0.46 (0.67), residues: 63 loop : -0.84 (0.50), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 21 HIS 0.004 0.001 HIS A 586 PHE 0.009 0.001 PHE A 305 TYR 0.014 0.001 TYR A 91 ARG 0.003 0.000 ARG A 17 *********************** 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 60 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.598 Fit side-chains REVERT: A 89 TYR cc_start: 0.7880 (m-10) cc_final: 0.7541 (m-10) REVERT: A 290 ASP cc_start: 0.8056 (t0) cc_final: 0.7786 (t0) outliers start: 10 outliers final: 5 residues processed: 57 average time/residue: 0.1581 time to fit residues: 14.0814 Evaluate side-chains 52 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 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 51 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 61 optimal weight: 30.0000 chunk 31 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 65 optimal weight: 20.0000 chunk 50 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 HIS ** 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 = 0.3857 r_free = 0.3857 target = 0.126807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.086734 restraints weight = 20866.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.089278 restraints weight = 9144.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.090857 restraints weight = 6187.931| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 9771 Z= 0.521 Angle : 0.783 10.837 14459 Z= 0.400 Chirality : 0.044 0.289 1819 Planarity : 0.005 0.045 887 Dihedral : 25.407 177.942 4362 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.70 % Allowed : 20.00 % Favored : 77.30 % 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: 0.91 (0.40), residues: 446 helix: 1.90 (0.33), residues: 242 sheet: -0.47 (0.69), residues: 64 loop : -1.18 (0.48), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 21 HIS 0.005 0.002 HIS A 586 PHE 0.016 0.003 PHE A 347 TYR 0.019 0.003 TYR A 441 ARG 0.004 0.001 ARG A 525 *********************** 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 49 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.616 Fit side-chains REVERT: A 89 TYR cc_start: 0.8084 (m-10) cc_final: 0.7744 (m-10) REVERT: A 290 ASP cc_start: 0.8057 (t0) cc_final: 0.7779 (t0) outliers start: 10 outliers final: 7 residues processed: 46 average time/residue: 0.1379 time to fit residues: 10.5712 Evaluate side-chains 43 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 284 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 463 VAL 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 68 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 4 optimal weight: 0.3980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.133044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.093557 restraints weight = 21300.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.096387 restraints weight = 8952.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.098116 restraints weight = 5914.368| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3693 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= 0.161 Angle : 0.575 10.305 14459 Z= 0.296 Chirality : 0.034 0.236 1819 Planarity : 0.004 0.038 887 Dihedral : 25.174 179.780 4362 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.16 % Allowed : 21.08 % Favored : 76.76 % 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: 1.42 (0.41), residues: 446 helix: 2.32 (0.34), residues: 242 sheet: -0.41 (0.67), residues: 64 loop : -0.86 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 21 HIS 0.004 0.001 HIS A 304 PHE 0.009 0.002 PHE A 13 TYR 0.017 0.001 TYR A 91 ARG 0.002 0.000 ARG A 350 ********************** 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 54 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.597 Fit side-chains REVERT: A 89 TYR cc_start: 0.7912 (m-10) cc_final: 0.7569 (m-10) REVERT: A 290 ASP cc_start: 0.8051 (t0) cc_final: 0.7714 (t0) outliers start: 8 outliers final: 7 residues processed: 51 average time/residue: 0.1354 time to fit residues: 11.3609 Evaluate side-chains 52 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 284 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 463 VAL 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 13 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 21 optimal weight: 0.3980 chunk 65 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 54 optimal weight: 20.0000 chunk 43 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3923 r_free = 0.3923 target = 0.131632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.093444 restraints weight = 21158.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.095996 restraints weight = 10980.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.096035 restraints weight = 6483.054| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9771 Z= 0.230 Angle : 0.598 10.327 14459 Z= 0.308 Chirality : 0.036 0.230 1819 Planarity : 0.004 0.037 887 Dihedral : 25.172 179.434 4362 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.89 % Allowed : 20.81 % Favored : 77.30 % 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: 1.34 (0.41), residues: 446 helix: 2.25 (0.33), residues: 242 sheet: -0.44 (0.67), residues: 64 loop : -0.91 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 356 HIS 0.003 0.001 HIS A 304 PHE 0.011 0.002 PHE A 305 TYR 0.013 0.002 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: 2519.61 seconds wall clock time: 46 minutes 8.51 seconds (2768.51 seconds total)