Starting phenix.real_space_refine on Fri Dec 8 08:25:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xht_33198/12_2023/7xht_33198_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xht_33198/12_2023/7xht_33198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xht_33198/12_2023/7xht_33198.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xht_33198/12_2023/7xht_33198.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xht_33198/12_2023/7xht_33198_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xht_33198/12_2023/7xht_33198_updated.pdb" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.177 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 220 5.49 5 Mg 2 5.21 5 S 19 5.16 5 C 4108 2.51 5 N 1449 2.21 5 O 2041 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7839 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 3822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 3822 Classifications: {'RNA': 179} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 12, 'rna3p_pur': 84, 'rna3p_pyr': 69} Link IDs: {'rna2p': 26, 'rna3p': 152} Chain breaks: 3 Chain: "C" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 595 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "D" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 249 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 3155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3155 Classifications: {'peptide': 395} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 376} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 17 Unusual residues: {' MG': 1, 'LDA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.27, per 1000 atoms: 0.67 Number of scatterers: 7839 At special positions: 0 Unit cell: (85.49, 110.39, 130.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 19 16.00 P 220 15.00 Mg 2 11.99 O 2041 8.00 N 1449 7.00 C 4108 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 - 3.50 Amino acid : False - 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: 4.60 Conformation dependent library (CDL) restraints added in 691.7 milliseconds 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 740 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 10 helices and 6 sheets defined 29.4% alpha, 18.5% beta 82 base pairs and 138 stacking pairs defined. Time for finding SS restraints: 4.02 Creating SS restraints... Processing helix chain 'A' and resid 21 through 29 Processing helix chain 'A' and resid 88 through 108 Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 111 through 121 Processing helix chain 'A' and resid 165 through 184 removed outlier: 3.670A pdb=" N VAL A 178 " --> pdb=" O HIS A 174 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 314 Proline residue: A 305 - end of helix Processing helix chain 'A' and resid 324 through 334 Processing helix chain 'A' and resid 340 through 351 removed outlier: 4.365A pdb=" N ALA A 344 " --> pdb=" O TYR A 341 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A 348 " --> pdb=" O TYR A 345 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N CYS A 349 " --> pdb=" O CYS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 419 through 423 Processing helix chain 'A' and resid 480 through 482 No H-bonds generated for 'chain 'A' and resid 480 through 482' Processing sheet with id= A, first strand: chain 'A' and resid 6 through 8 removed outlier: 6.604A pdb=" N GLN A 44 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL A 35 " --> pdb=" O GLN A 44 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.407A pdb=" N VAL A 190 " --> pdb=" O CYS A 320 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N THR A 322 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU A 192 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 80 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR A 73 " --> pdb=" O SER A 78 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER A 78 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N TYR A 366 " --> pdb=" O GLN A 83 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N GLU A 85 " --> pdb=" O TYR A 366 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL A 368 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 129 through 132 Processing sheet with id= D, first strand: chain 'A' and resid 426 through 428 removed outlier: 3.521A pdb=" N ALA A 396 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N MET A 390 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LEU A 394 " --> pdb=" O MET A 390 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 453 through 455 removed outlier: 6.356A pdb=" N VAL A 447 " --> pdb=" O TYR A 485 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N TYR A 485 " --> pdb=" O VAL A 447 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 477 through 479 109 hydrogen bonds defined for protein. 288 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 208 hydrogen bonds 388 hydrogen bond angles 0 basepair planarities 82 basepair parallelities 138 stacking parallelities Total time for adding SS restraints: 3.80 Time building geometry restraints manager: 4.74 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: 1283 1.33 - 1.45: 3178 1.45 - 1.57: 3525 1.57 - 1.69: 434 1.69 - 1.81: 29 Bond restraints: 8449 Sorted by residual: bond pdb=" N1 LDA A 501 " pdb=" O1 LDA A 501 " ideal model delta sigma weight residual 1.354 1.249 0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" C1 LDA A 501 " pdb=" N1 LDA A 501 " ideal model delta sigma weight residual 1.503 1.454 0.049 2.00e-02 2.50e+03 6.03e+00 bond pdb=" O3' DC D 8 " pdb=" P DC D 9 " ideal model delta sigma weight residual 1.607 1.579 0.028 1.50e-02 4.44e+03 3.56e+00 bond pdb=" O3' A B 195 " pdb=" P A B 196 " ideal model delta sigma weight residual 1.607 1.579 0.028 1.50e-02 4.44e+03 3.42e+00 bond pdb=" O3' DG C 16 " pdb=" P DC C 17 " ideal model delta sigma weight residual 1.607 1.580 0.027 1.50e-02 4.44e+03 3.19e+00 ... (remaining 8444 not shown) Histogram of bond angle deviations from ideal: 81.20 - 91.76: 2 91.76 - 102.32: 267 102.32 - 112.87: 5676 112.87 - 123.43: 5418 123.43 - 133.99: 1082 Bond angle restraints: 12445 Sorted by residual: angle pdb=" O3' DT C 10 " pdb=" P DT C 11 " pdb=" OP1 DT C 11 " ideal model delta sigma weight residual 108.00 81.20 26.80 3.00e+00 1.11e-01 7.98e+01 angle pdb=" O3' DT C 10 " pdb=" P DT C 11 " pdb=" O5' DT C 11 " ideal model delta sigma weight residual 104.00 115.97 -11.97 1.50e+00 4.44e-01 6.36e+01 angle pdb=" O3' DT C 11 " pdb=" P DA C 12 " pdb=" OP1 DA C 12 " ideal model delta sigma weight residual 108.00 89.06 18.94 3.00e+00 1.11e-01 3.99e+01 angle pdb=" C3' DT C 11 " pdb=" O3' DT C 11 " pdb=" P DA C 12 " ideal model delta sigma weight residual 120.20 110.80 9.40 1.50e+00 4.44e-01 3.93e+01 angle pdb=" O3' DT C 11 " pdb=" P DA C 12 " pdb=" O5' DA C 12 " ideal model delta sigma weight residual 104.00 113.30 -9.30 1.50e+00 4.44e-01 3.84e+01 ... (remaining 12440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.65: 4551 33.65 - 67.30: 448 67.30 - 100.95: 53 100.95 - 134.60: 0 134.60 - 168.25: 2 Dihedral angle restraints: 5054 sinusoidal: 3905 harmonic: 1149 Sorted by residual: dihedral pdb=" O4' U B 92 " pdb=" C1' U B 92 " pdb=" N1 U B 92 " pdb=" C2 U B 92 " ideal model delta sinusoidal sigma weight residual 232.00 94.55 137.45 1 1.70e+01 3.46e-03 5.77e+01 dihedral pdb=" C4' G B 76 " pdb=" C3' G B 76 " pdb=" O3' G B 76 " pdb=" P A B 77 " ideal model delta sinusoidal sigma weight residual 220.00 51.75 168.25 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" CA ASN A 148 " pdb=" C ASN A 148 " pdb=" N LYS A 149 " pdb=" CA LYS A 149 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 5051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1390 0.056 - 0.112: 126 0.112 - 0.168: 12 0.168 - 0.224: 0 0.224 - 0.280: 1 Chirality restraints: 1529 Sorted by residual: chirality pdb=" CB ILE A 146 " pdb=" CA ILE A 146 " pdb=" CG1 ILE A 146 " pdb=" CG2 ILE A 146 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C1' A B 81 " pdb=" O4' A B 81 " pdb=" C2' A B 81 " pdb=" N9 A B 81 " both_signs ideal model delta sigma weight residual False 2.46 2.30 0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" C3' G B 76 " pdb=" C4' G B 76 " pdb=" O3' G B 76 " pdb=" C2' G B 76 " both_signs ideal model delta sigma weight residual False -2.48 -2.34 -0.14 2.00e-01 2.50e+01 4.96e-01 ... (remaining 1526 not shown) Planarity restraints: 776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B 51 " 0.030 2.00e-02 2.50e+03 1.30e-02 4.66e+00 pdb=" N9 A B 51 " -0.027 2.00e-02 2.50e+03 pdb=" C8 A B 51 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A B 51 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A B 51 " -0.004 2.00e-02 2.50e+03 pdb=" C6 A B 51 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A B 51 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A B 51 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A B 51 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A B 51 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A B 51 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B -8 " -0.028 2.00e-02 2.50e+03 1.41e-02 4.45e+00 pdb=" N1 C B -8 " 0.029 2.00e-02 2.50e+03 pdb=" C2 C B -8 " 0.004 2.00e-02 2.50e+03 pdb=" O2 C B -8 " 0.005 2.00e-02 2.50e+03 pdb=" N3 C B -8 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C B -8 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C B -8 " -0.007 2.00e-02 2.50e+03 pdb=" C5 C B -8 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C B -8 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 112 " -0.022 2.00e-02 2.50e+03 1.08e-02 3.19e+00 pdb=" N9 A B 112 " 0.027 2.00e-02 2.50e+03 pdb=" C8 A B 112 " 0.000 2.00e-02 2.50e+03 pdb=" N7 A B 112 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A B 112 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A B 112 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A B 112 " -0.004 2.00e-02 2.50e+03 pdb=" N1 A B 112 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A B 112 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A B 112 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A B 112 " 0.002 2.00e-02 2.50e+03 ... (remaining 773 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 67 2.59 - 3.17: 5677 3.17 - 3.75: 15129 3.75 - 4.32: 21465 4.32 - 4.90: 28207 Nonbonded interactions: 70545 Sorted by model distance: nonbonded pdb=" OD1 ASP A 61 " pdb="MG MG A 502 " model vdw 2.014 2.170 nonbonded pdb=" O2' A B 69 " pdb=" O4' A B 70 " model vdw 2.139 2.440 nonbonded pdb=" OP1 U B 190 " pdb=" OH TYR A 47 " model vdw 2.204 2.440 nonbonded pdb=" O2' C B 82 " pdb=" O ASN A 155 " model vdw 2.222 2.440 nonbonded pdb=" O2' G B 76 " pdb=" O5' A B 77 " model vdw 2.230 2.440 ... (remaining 70540 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.510 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 29.070 Find NCS groups from input model: 0.150 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:13.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 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 0.105 8449 Z= 0.191 Angle : 0.680 26.798 12445 Z= 0.350 Chirality : 0.033 0.280 1529 Planarity : 0.005 0.038 776 Dihedral : 20.463 168.253 4314 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.35 (0.42), residues: 391 helix: 1.08 (0.50), residues: 120 sheet: 0.76 (0.61), residues: 72 loop : -0.45 (0.41), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 479 HIS 0.006 0.001 HIS A 105 PHE 0.009 0.001 PHE A 315 TYR 0.017 0.002 TYR A 6 ARG 0.004 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.615 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 1.4870 time to fit residues: 115.4448 Evaluate side-chains 50 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.551 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 100 GLN A 131 GLN A 169 HIS A 195 ASN A 405 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8449 Z= 0.200 Angle : 0.536 7.624 12445 Z= 0.293 Chirality : 0.033 0.209 1529 Planarity : 0.005 0.040 776 Dihedral : 21.471 168.419 3507 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.17 % Allowed : 10.53 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.46 (0.42), residues: 391 helix: 1.21 (0.51), residues: 120 sheet: 0.66 (0.61), residues: 72 loop : -0.33 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 479 HIS 0.005 0.001 HIS A 105 PHE 0.005 0.001 PHE A 315 TYR 0.017 0.002 TYR A 6 ARG 0.007 0.001 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.580 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 52 average time/residue: 1.5683 time to fit residues: 86.0160 Evaluate side-chains 49 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.689 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.9634 time to fit residues: 3.1278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8449 Z= 0.275 Angle : 0.590 7.765 12445 Z= 0.319 Chirality : 0.036 0.170 1529 Planarity : 0.005 0.043 776 Dihedral : 21.483 169.669 3507 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.05 % Allowed : 11.40 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.40 (0.42), residues: 391 helix: 1.10 (0.50), residues: 120 sheet: 0.53 (0.60), residues: 72 loop : -0.29 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 479 HIS 0.003 0.001 HIS A 105 PHE 0.006 0.001 PHE A 315 TYR 0.019 0.002 TYR A 6 ARG 0.005 0.001 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.547 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 49 average time/residue: 1.5273 time to fit residues: 78.7080 Evaluate side-chains 47 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.443 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 3 average time/residue: 0.3979 time to fit residues: 1.9738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 0.1980 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 32 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN A 405 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8449 Z= 0.134 Angle : 0.497 7.388 12445 Z= 0.273 Chirality : 0.031 0.165 1529 Planarity : 0.004 0.042 776 Dihedral : 21.380 167.686 3507 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.75 % Allowed : 13.16 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.64 (0.42), residues: 391 helix: 1.37 (0.49), residues: 120 sheet: 0.48 (0.60), residues: 72 loop : -0.11 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 162 HIS 0.003 0.001 HIS A 105 PHE 0.004 0.001 PHE A 41 TYR 0.018 0.001 TYR A 341 ARG 0.005 0.000 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.544 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 43 average time/residue: 1.4855 time to fit residues: 67.5238 Evaluate side-chains 48 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.564 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 2 residues processed: 4 average time/residue: 0.4016 time to fit residues: 2.5873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 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 405 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8449 Z= 0.267 Angle : 0.580 7.791 12445 Z= 0.313 Chirality : 0.035 0.146 1529 Planarity : 0.005 0.043 776 Dihedral : 21.427 169.598 3507 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.34 % Allowed : 14.04 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.55 (0.42), residues: 391 helix: 1.28 (0.49), residues: 120 sheet: 0.45 (0.61), residues: 72 loop : -0.16 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 479 HIS 0.003 0.001 HIS A 429 PHE 0.006 0.001 PHE A 315 TYR 0.021 0.002 TYR A 341 ARG 0.004 0.001 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.578 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 49 average time/residue: 1.4837 time to fit residues: 76.6569 Evaluate side-chains 49 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.525 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 0.4064 time to fit residues: 1.9615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 41 optimal weight: 0.1980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8449 Z= 0.250 Angle : 0.569 7.801 12445 Z= 0.308 Chirality : 0.035 0.146 1529 Planarity : 0.005 0.044 776 Dihedral : 21.420 169.599 3507 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.05 % Allowed : 14.91 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.51 (0.42), residues: 391 helix: 1.28 (0.49), residues: 120 sheet: 0.42 (0.61), residues: 72 loop : -0.20 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 162 HIS 0.003 0.001 HIS A 429 PHE 0.006 0.001 PHE A 315 TYR 0.021 0.002 TYR A 341 ARG 0.004 0.001 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.568 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 47 average time/residue: 1.4083 time to fit residues: 69.8696 Evaluate side-chains 48 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.488 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 0.3917 time to fit residues: 1.8961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 0.0060 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 56 optimal weight: 0.0070 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 0.3980 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.8016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8449 Z= 0.155 Angle : 0.527 7.690 12445 Z= 0.289 Chirality : 0.032 0.155 1529 Planarity : 0.004 0.043 776 Dihedral : 21.408 168.748 3507 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.05 % Allowed : 15.50 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.63 (0.42), residues: 391 helix: 1.48 (0.50), residues: 120 sheet: 0.46 (0.61), residues: 71 loop : -0.18 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 162 HIS 0.003 0.001 HIS A 105 PHE 0.005 0.001 PHE A 125 TYR 0.020 0.002 TYR A 341 ARG 0.002 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.685 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 45 average time/residue: 1.3957 time to fit residues: 66.5040 Evaluate side-chains 47 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.535 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.0680 time to fit residues: 0.8046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 49 optimal weight: 0.0670 chunk 52 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8449 Z= 0.173 Angle : 0.526 7.842 12445 Z= 0.287 Chirality : 0.033 0.157 1529 Planarity : 0.004 0.043 776 Dihedral : 21.396 168.849 3507 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.46 % Allowed : 16.08 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.67 (0.42), residues: 391 helix: 1.51 (0.49), residues: 120 sheet: 0.45 (0.61), residues: 71 loop : -0.14 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 162 HIS 0.003 0.001 HIS A 105 PHE 0.004 0.001 PHE A 41 TYR 0.024 0.002 TYR A 341 ARG 0.002 0.000 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.583 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 45 average time/residue: 1.3889 time to fit residues: 66.1110 Evaluate side-chains 47 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.533 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.0699 time to fit residues: 0.8707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 16 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 0.1980 chunk 58 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8449 Z= 0.151 Angle : 0.512 7.580 12445 Z= 0.282 Chirality : 0.032 0.153 1529 Planarity : 0.004 0.043 776 Dihedral : 21.388 168.518 3507 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.75 % Allowed : 15.50 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.72 (0.42), residues: 391 helix: 1.56 (0.50), residues: 120 sheet: 0.47 (0.62), residues: 71 loop : -0.12 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 162 HIS 0.003 0.001 HIS A 105 PHE 0.004 0.001 PHE A 125 TYR 0.022 0.002 TYR A 341 ARG 0.002 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.513 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 46 average time/residue: 1.3348 time to fit residues: 64.9760 Evaluate side-chains 45 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.509 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.5631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 0.0020 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8449 Z= 0.229 Angle : 0.553 7.724 12445 Z= 0.300 Chirality : 0.034 0.148 1529 Planarity : 0.005 0.042 776 Dihedral : 21.391 169.371 3507 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.46 % Allowed : 14.91 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.65 (0.42), residues: 391 helix: 1.48 (0.49), residues: 120 sheet: 0.48 (0.62), residues: 71 loop : -0.16 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 162 HIS 0.002 0.001 HIS A 429 PHE 0.006 0.001 PHE A 315 TYR 0.023 0.002 TYR A 341 ARG 0.003 0.001 ARG A 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.563 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 49 average time/residue: 1.4034 time to fit residues: 72.7071 Evaluate side-chains 47 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.566 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.0744 time to fit residues: 0.7636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 33 optimal weight: 0.0670 chunk 53 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.175997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.123437 restraints weight = 5441.330| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 0.60 r_work: 0.3118 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8449 Z= 0.143 Angle : 0.518 7.617 12445 Z= 0.284 Chirality : 0.032 0.156 1529 Planarity : 0.004 0.043 776 Dihedral : 21.384 168.442 3507 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.75 % Allowed : 15.50 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.74 (0.42), residues: 391 helix: 1.63 (0.50), residues: 120 sheet: 0.47 (0.62), residues: 71 loop : -0.13 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 162 HIS 0.003 0.001 HIS A 105 PHE 0.005 0.001 PHE A 125 TYR 0.024 0.002 TYR A 341 ARG 0.002 0.000 ARG A 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2443.84 seconds wall clock time: 44 minutes 42.71 seconds (2682.71 seconds total)