Starting phenix.real_space_refine on Mon Sep 23 14:41:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb5_32395/09_2024/7wb5_32395.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb5_32395/09_2024/7wb5_32395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb5_32395/09_2024/7wb5_32395.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb5_32395/09_2024/7wb5_32395.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb5_32395/09_2024/7wb5_32395.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wb5_32395/09_2024/7wb5_32395.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2077 2.51 5 N 533 2.21 5 O 631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3256 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "R" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1465 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.75, per 1000 atoms: 1.15 Number of scatterers: 3256 At special positions: 0 Unit cell: (72.36, 88.56, 72.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 631 8.00 N 533 7.00 C 2077 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.04 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.02 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " NAG-ASN " NAG A 1 " - " ASN R 343 " Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 393.3 milliseconds 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 12 sheets defined 4.4% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'R' and resid 349 through 353 Processing helix chain 'R' and resid 364 through 370 removed outlier: 4.598A pdb=" N LEU R 368 " --> pdb=" O ASP R 364 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 421 Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.682A pdb=" N LYS H 12 " --> pdb=" O THR H 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'H' and resid 46 through 47 removed outlier: 3.906A pdb=" N THR H 113 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 49 through 51 removed outlier: 3.533A pdb=" N TRP H 50 " --> pdb=" O THR H 59 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 68 through 70 Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.846A pdb=" N ILE L 21 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU L 73 " --> pdb=" O ILE L 21 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.595A pdb=" N LEU L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.572A pdb=" N GLN L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.884A pdb=" N ILE R 434 " --> pdb=" O VAL R 511 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N CYS R 432 " --> pdb=" O LEU R 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 354 through 358 Processing sheet with id=AB2, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'R' and resid 473 through 474 73 hydrogen bonds defined for protein. 171 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.86 Time building geometry restraints manager: 1.15 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: 734 1.33 - 1.45: 857 1.45 - 1.57: 1735 1.57 - 1.69: 1 1.69 - 1.82: 18 Bond restraints: 3345 Sorted by residual: bond pdb=" CA SER R 438 " pdb=" CB SER R 438 " ideal model delta sigma weight residual 1.528 1.475 0.053 1.35e-02 5.49e+03 1.53e+01 bond pdb=" CA SER R 349 " pdb=" CB SER R 349 " ideal model delta sigma weight residual 1.529 1.467 0.062 1.64e-02 3.72e+03 1.43e+01 bond pdb=" N LEU R 452 " pdb=" CA LEU R 452 " ideal model delta sigma weight residual 1.452 1.495 -0.043 1.22e-02 6.72e+03 1.23e+01 bond pdb=" N VAL R 433 " pdb=" CA VAL R 433 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.07e+01 bond pdb=" N LYS R 378 " pdb=" CA LYS R 378 " ideal model delta sigma weight residual 1.457 1.499 -0.041 1.29e-02 6.01e+03 1.03e+01 ... (remaining 3340 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 4160 2.59 - 5.17: 364 5.17 - 7.76: 19 7.76 - 10.34: 3 10.34 - 12.93: 2 Bond angle restraints: 4548 Sorted by residual: angle pdb=" CA PRO L 80 " pdb=" N PRO L 80 " pdb=" CD PRO L 80 " ideal model delta sigma weight residual 112.00 99.07 12.93 1.40e+00 5.10e-01 8.52e+01 angle pdb=" CA TRP R 436 " pdb=" CB TRP R 436 " pdb=" CG TRP R 436 " ideal model delta sigma weight residual 113.60 123.83 -10.23 1.90e+00 2.77e-01 2.90e+01 angle pdb=" CA PHE R 400 " pdb=" CB PHE R 400 " pdb=" CG PHE R 400 " ideal model delta sigma weight residual 113.80 118.30 -4.50 1.00e+00 1.00e+00 2.03e+01 angle pdb=" N PRO L 80 " pdb=" CD PRO L 80 " pdb=" CG PRO L 80 " ideal model delta sigma weight residual 103.20 96.90 6.30 1.50e+00 4.44e-01 1.77e+01 angle pdb=" N LEU R 387 " pdb=" CA LEU R 387 " pdb=" C LEU R 387 " ideal model delta sigma weight residual 114.75 109.56 5.19 1.26e+00 6.30e-01 1.69e+01 ... (remaining 4543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.52: 1718 21.52 - 43.04: 173 43.04 - 64.55: 66 64.55 - 86.07: 12 86.07 - 107.59: 12 Dihedral angle restraints: 1981 sinusoidal: 801 harmonic: 1180 Sorted by residual: dihedral pdb=" CA VAL L 29 " pdb=" C VAL L 29 " pdb=" N SER L 30 " pdb=" CA SER L 30 " ideal model delta harmonic sigma weight residual 180.00 -139.90 -40.10 0 5.00e+00 4.00e-02 6.43e+01 dihedral pdb=" CA PHE H 106 " pdb=" C PHE H 106 " pdb=" N ASP H 107 " pdb=" CA ASP H 107 " ideal model delta harmonic sigma weight residual 180.00 -146.68 -33.32 0 5.00e+00 4.00e-02 4.44e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 136.78 -43.78 1 1.00e+01 1.00e-02 2.67e+01 ... (remaining 1978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 417 0.119 - 0.238: 63 0.238 - 0.356: 5 0.356 - 0.475: 0 0.475 - 0.593: 2 Chirality restraints: 487 Sorted by residual: chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 6.89e+01 chirality pdb=" C1 BMA A 3 " pdb=" O4 NAG A 2 " pdb=" C2 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.29e+01 chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN R 343 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.81e+00 ... (remaining 484 not shown) Planarity restraints: 582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 2 " 0.304 2.00e-02 2.50e+03 2.62e-01 8.61e+02 pdb=" C7 NAG A 2 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG A 2 " 0.009 2.00e-02 2.50e+03 pdb=" N2 NAG A 2 " -0.453 2.00e-02 2.50e+03 pdb=" O7 NAG A 2 " 0.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " -0.292 2.00e-02 2.50e+03 2.51e-01 7.91e+02 pdb=" C7 NAG A 1 " 0.068 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " -0.164 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " 0.443 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN L 79 " -0.111 5.00e-02 4.00e+02 1.57e-01 3.92e+01 pdb=" N PRO L 80 " 0.270 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " -0.076 5.00e-02 4.00e+02 ... (remaining 579 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 281 2.73 - 3.27: 3255 3.27 - 3.82: 5356 3.82 - 4.36: 6706 4.36 - 4.90: 11080 Nonbonded interactions: 26678 Sorted by model distance: nonbonded pdb=" O ILE L 21 " pdb=" OG1 THR L 72 " model vdw 2.188 3.040 nonbonded pdb=" OG SER H 7 " pdb=" OG SER H 21 " model vdw 2.216 3.040 nonbonded pdb=" OE1 GLN H 6 " pdb=" OG1 THR H 113 " model vdw 2.319 3.040 nonbonded pdb=" OG SER L 26 " pdb=" OE1 GLN L 27 " model vdw 2.405 3.040 nonbonded pdb=" O VAL H 76 " pdb=" OG SER H 77 " model vdw 2.421 3.040 ... (remaining 26673 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: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.650 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 : 0.011 0.132 3345 Z= 0.690 Angle : 1.407 12.925 4548 Z= 0.926 Chirality : 0.090 0.593 487 Planarity : 0.018 0.262 581 Dihedral : 21.949 107.591 1220 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 2.24 % Allowed : 18.16 % Favored : 79.60 % Rotamer: Outliers : 14.00 % Allowed : 7.43 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -4.90 (0.36), residues: 402 helix: -4.22 (0.64), residues: 21 sheet: -3.58 (0.39), residues: 121 loop : -3.14 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.006 TRP H 109 HIS 0.001 0.001 HIS L 34 PHE 0.023 0.003 PHE R 400 TYR 0.024 0.003 TYR L 49 ARG 0.007 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 125 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: H 83 ILE cc_start: 0.9173 (tt) cc_final: 0.8932 (tt) REVERT: L 74 THR cc_start: 0.7091 (m) cc_final: 0.6553 (m) REVERT: L 79 GLN cc_start: 0.8296 (mp10) cc_final: 0.7818 (mp10) REVERT: R 369 TYR cc_start: 0.7978 (t80) cc_final: 0.7755 (t80) REVERT: R 387 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8498 (tt) REVERT: R 454 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7654 (mtp-110) REVERT: R 493 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7989 (tm-30) outliers start: 49 outliers final: 12 residues processed: 150 average time/residue: 0.1915 time to fit residues: 33.7700 Evaluate side-chains 122 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain R residue 422 ASN Chi-restraints excluded: chain R residue 425 LEU Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 436 TRP Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 454 ARG Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 493 GLN Chi-restraints excluded: chain R residue 516 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 ASN H 82 GLN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 481 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3345 Z= 0.261 Angle : 0.817 8.195 4548 Z= 0.416 Chirality : 0.050 0.188 487 Planarity : 0.007 0.084 581 Dihedral : 17.669 92.973 544 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.20 % Favored : 89.30 % Rotamer: Outliers : 7.71 % Allowed : 18.00 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -4.48 (0.36), residues: 402 helix: -3.44 (0.77), residues: 21 sheet: -3.11 (0.42), residues: 114 loop : -3.03 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP H 109 HIS 0.002 0.001 HIS L 34 PHE 0.027 0.002 PHE R 515 TYR 0.019 0.002 TYR L 49 ARG 0.006 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.8422 (m-80) cc_final: 0.8067 (m-10) REVERT: L 79 GLN cc_start: 0.8409 (mp10) cc_final: 0.7675 (mp10) REVERT: R 387 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8382 (tt) REVERT: R 462 LYS cc_start: 0.8533 (pptt) cc_final: 0.8093 (ptmm) REVERT: R 493 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7735 (tm-30) REVERT: R 516 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7450 (pp20) outliers start: 27 outliers final: 19 residues processed: 123 average time/residue: 0.1849 time to fit residues: 26.7545 Evaluate side-chains 120 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 422 ASN Chi-restraints excluded: chain R residue 425 LEU Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 436 TRP Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 452 LEU Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain R residue 493 GLN Chi-restraints excluded: chain R residue 495 TYR Chi-restraints excluded: chain R residue 516 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 0.1980 chunk 9 optimal weight: 0.3980 chunk 35 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 26 optimal weight: 0.0030 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3345 Z= 0.222 Angle : 0.748 9.741 4548 Z= 0.372 Chirality : 0.049 0.229 487 Planarity : 0.006 0.078 581 Dihedral : 14.787 80.524 538 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.95 % Favored : 88.56 % Rotamer: Outliers : 6.57 % Allowed : 19.14 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -4.06 (0.37), residues: 402 helix: -3.73 (0.70), residues: 21 sheet: -2.43 (0.46), residues: 114 loop : -2.89 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP H 109 HIS 0.002 0.001 HIS L 34 PHE 0.024 0.002 PHE R 515 TYR 0.021 0.002 TYR H 105 ARG 0.004 0.001 ARG R 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.8307 (m-80) cc_final: 0.8068 (m-10) REVERT: L 79 GLN cc_start: 0.8448 (mp10) cc_final: 0.8031 (mp10) REVERT: L 100 GLN cc_start: 0.7333 (tm-30) cc_final: 0.7113 (tm-30) REVERT: R 386 LYS cc_start: 0.4618 (pttt) cc_final: 0.3250 (pttt) REVERT: R 387 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8290 (tt) REVERT: R 462 LYS cc_start: 0.8473 (pptt) cc_final: 0.8084 (ptmm) REVERT: R 493 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7456 (tm-30) outliers start: 23 outliers final: 20 residues processed: 126 average time/residue: 0.1769 time to fit residues: 26.1825 Evaluate side-chains 119 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 452 LEU Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 0.0970 chunk 21 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 3345 Z= 0.407 Angle : 0.807 8.388 4548 Z= 0.411 Chirality : 0.050 0.249 487 Planarity : 0.007 0.085 581 Dihedral : 12.500 65.214 526 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.50 % Allowed : 11.69 % Favored : 87.81 % Rotamer: Outliers : 9.14 % Allowed : 20.57 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -4.21 (0.37), residues: 402 helix: -3.58 (0.83), residues: 19 sheet: -2.89 (0.42), residues: 127 loop : -2.78 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP H 109 HIS 0.003 0.002 HIS L 34 PHE 0.020 0.002 PHE R 392 TYR 0.027 0.002 TYR L 49 ARG 0.006 0.001 ARG R 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 91 time to evaluate : 0.371 Fit side-chains REVERT: H 34 MET cc_start: 0.8995 (tpp) cc_final: 0.8719 (tpp) REVERT: H 60 TYR cc_start: 0.8558 (m-80) cc_final: 0.8267 (m-10) REVERT: L 62 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7371 (p90) REVERT: L 79 GLN cc_start: 0.8488 (mp10) cc_final: 0.8099 (mp10) REVERT: L 100 GLN cc_start: 0.7479 (tm-30) cc_final: 0.7123 (tm-30) REVERT: R 387 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8475 (tt) REVERT: R 493 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7506 (tm-30) REVERT: R 508 TYR cc_start: 0.6759 (m-80) cc_final: 0.6109 (m-80) outliers start: 32 outliers final: 23 residues processed: 110 average time/residue: 0.1680 time to fit residues: 21.8216 Evaluate side-chains 113 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 88 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 393 THR Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 436 TRP Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 452 LEU Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 437 ASN R 450 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3345 Z= 0.267 Angle : 0.735 8.896 4548 Z= 0.371 Chirality : 0.047 0.207 487 Planarity : 0.006 0.081 581 Dihedral : 10.742 57.485 526 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.95 % Favored : 88.81 % Rotamer: Outliers : 8.57 % Allowed : 22.29 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -4.07 (0.37), residues: 402 helix: -3.58 (0.86), residues: 19 sheet: -2.75 (0.44), residues: 123 loop : -2.72 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP H 109 HIS 0.001 0.001 HIS L 34 PHE 0.015 0.002 PHE R 392 TYR 0.022 0.002 TYR H 105 ARG 0.005 0.001 ARG R 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 95 time to evaluate : 0.382 Fit side-chains REVERT: H 43 GLN cc_start: 0.7144 (mp10) cc_final: 0.6689 (mp10) REVERT: H 60 TYR cc_start: 0.8402 (m-80) cc_final: 0.8149 (m-10) REVERT: L 62 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7271 (p90) REVERT: L 79 GLN cc_start: 0.8469 (mp10) cc_final: 0.8031 (mp10) REVERT: L 100 GLN cc_start: 0.7450 (tm-30) cc_final: 0.7148 (tm-30) REVERT: R 387 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8396 (tt) REVERT: R 408 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8023 (ptm160) REVERT: R 409 GLN cc_start: 0.8428 (mt0) cc_final: 0.7757 (mt0) REVERT: R 453 TYR cc_start: 0.8739 (p90) cc_final: 0.8325 (p90) REVERT: R 493 GLN cc_start: 0.8150 (tm-30) cc_final: 0.7520 (tm-30) REVERT: R 508 TYR cc_start: 0.6472 (m-80) cc_final: 0.6141 (m-80) outliers start: 30 outliers final: 21 residues processed: 114 average time/residue: 0.1683 time to fit residues: 22.7616 Evaluate side-chains 113 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 89 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 TRP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 408 ARG Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 452 LEU Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain R residue 495 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 4 optimal weight: 0.0040 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3345 Z= 0.232 Angle : 0.725 8.058 4548 Z= 0.367 Chirality : 0.047 0.195 487 Planarity : 0.006 0.080 581 Dihedral : 9.390 53.751 521 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.95 % Favored : 89.80 % Rotamer: Outliers : 8.86 % Allowed : 22.86 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -4.03 (0.37), residues: 402 helix: -3.28 (0.93), residues: 19 sheet: -2.76 (0.43), residues: 125 loop : -2.69 (0.34), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP H 109 HIS 0.002 0.001 HIS L 34 PHE 0.012 0.001 PHE R 392 TYR 0.020 0.002 TYR H 105 ARG 0.004 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 97 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 GLN cc_start: 0.7108 (mp10) cc_final: 0.6570 (mp10) REVERT: H 60 TYR cc_start: 0.8356 (m-80) cc_final: 0.8107 (m-10) REVERT: L 62 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7257 (p90) REVERT: L 79 GLN cc_start: 0.8531 (mp10) cc_final: 0.8032 (mp10) REVERT: L 100 GLN cc_start: 0.7412 (tm-30) cc_final: 0.7152 (tm-30) REVERT: R 387 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8347 (tt) REVERT: R 408 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8089 (ptm160) REVERT: R 418 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8062 (mm) REVERT: R 453 TYR cc_start: 0.8658 (p90) cc_final: 0.8227 (p90) REVERT: R 493 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7651 (tm-30) outliers start: 31 outliers final: 23 residues processed: 116 average time/residue: 0.1853 time to fit residues: 25.2899 Evaluate side-chains 119 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 92 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 TRP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 408 ARG Chi-restraints excluded: chain R residue 418 ILE Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain R residue 495 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.2980 chunk 31 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 409 GLN ** R 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 3345 Z= 0.326 Angle : 0.790 11.649 4548 Z= 0.397 Chirality : 0.049 0.184 487 Planarity : 0.006 0.080 581 Dihedral : 9.133 57.148 521 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.70 % Favored : 89.05 % Rotamer: Outliers : 8.86 % Allowed : 23.14 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -4.04 (0.38), residues: 402 helix: -3.22 (1.02), residues: 19 sheet: -2.90 (0.42), residues: 124 loop : -2.62 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.004 TRP H 109 HIS 0.001 0.001 HIS L 34 PHE 0.011 0.002 PHE R 392 TYR 0.022 0.002 TYR H 105 ARG 0.004 0.001 ARG R 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 94 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: H 43 GLN cc_start: 0.7181 (mp10) cc_final: 0.6701 (mp10) REVERT: H 60 TYR cc_start: 0.8463 (m-80) cc_final: 0.7989 (m-10) REVERT: H 69 VAL cc_start: 0.8348 (t) cc_final: 0.7950 (t) REVERT: L 62 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7330 (p90) REVERT: L 79 GLN cc_start: 0.8564 (mp10) cc_final: 0.8008 (mp10) REVERT: L 100 GLN cc_start: 0.7468 (tm-30) cc_final: 0.7191 (tm-30) REVERT: R 387 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8404 (tt) REVERT: R 408 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8213 (ptm160) REVERT: R 453 TYR cc_start: 0.8672 (p90) cc_final: 0.8317 (p90) REVERT: R 493 GLN cc_start: 0.8110 (tm-30) cc_final: 0.7348 (tm-30) outliers start: 31 outliers final: 24 residues processed: 114 average time/residue: 0.1798 time to fit residues: 24.1175 Evaluate side-chains 120 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 93 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 TRP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 408 ARG Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 455 LEU Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 34 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3345 Z= 0.254 Angle : 0.760 11.156 4548 Z= 0.384 Chirality : 0.047 0.190 487 Planarity : 0.006 0.080 581 Dihedral : 8.806 58.042 521 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.70 % Favored : 89.05 % Rotamer: Outliers : 7.71 % Allowed : 24.29 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.87 (0.37), residues: 402 helix: -3.39 (0.93), residues: 19 sheet: -2.66 (0.44), residues: 116 loop : -2.59 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP H 109 HIS 0.001 0.001 HIS L 34 PHE 0.010 0.001 PHE R 392 TYR 0.022 0.002 TYR H 105 ARG 0.011 0.001 ARG H 65 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 95 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: H 60 TYR cc_start: 0.8326 (m-80) cc_final: 0.7993 (m-10) REVERT: H 104 TRP cc_start: 0.8696 (m100) cc_final: 0.8422 (m100) REVERT: L 62 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7295 (p90) REVERT: L 79 GLN cc_start: 0.8571 (mp10) cc_final: 0.7962 (mp10) REVERT: L 100 GLN cc_start: 0.7453 (tm-30) cc_final: 0.7228 (tm-30) REVERT: R 386 LYS cc_start: 0.4278 (pttt) cc_final: 0.2918 (pttt) REVERT: R 387 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8303 (tt) REVERT: R 408 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8318 (ptm-80) REVERT: R 418 ILE cc_start: 0.8389 (tp) cc_final: 0.8171 (tp) REVERT: R 453 TYR cc_start: 0.8610 (p90) cc_final: 0.8349 (p90) REVERT: R 466 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6870 (mtp-110) REVERT: R 493 GLN cc_start: 0.8077 (tm-30) cc_final: 0.7562 (tm-30) outliers start: 27 outliers final: 22 residues processed: 110 average time/residue: 0.1730 time to fit residues: 22.5914 Evaluate side-chains 118 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 92 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 TRP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 408 ARG Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 455 LEU Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3345 Z= 0.259 Angle : 0.763 10.754 4548 Z= 0.386 Chirality : 0.048 0.210 487 Planarity : 0.006 0.080 581 Dihedral : 8.525 56.726 521 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.95 % Favored : 89.80 % Rotamer: Outliers : 8.00 % Allowed : 24.00 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.80 (0.38), residues: 402 helix: -3.45 (0.92), residues: 19 sheet: -2.58 (0.42), residues: 124 loop : -2.51 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP H 109 HIS 0.001 0.001 HIS L 34 PHE 0.010 0.001 PHE R 392 TYR 0.023 0.002 TYR R 508 ARG 0.005 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 94 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: H 60 TYR cc_start: 0.8346 (m-80) cc_final: 0.7930 (m-10) REVERT: H 69 VAL cc_start: 0.8358 (t) cc_final: 0.7929 (t) REVERT: H 104 TRP cc_start: 0.8647 (m100) cc_final: 0.8415 (m100) REVERT: L 62 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7259 (p90) REVERT: L 79 GLN cc_start: 0.8584 (mp10) cc_final: 0.7962 (mp10) REVERT: L 100 GLN cc_start: 0.7420 (tm-30) cc_final: 0.7192 (tm-30) REVERT: R 387 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8341 (tt) REVERT: R 408 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8314 (ptm-80) REVERT: R 418 ILE cc_start: 0.8367 (tp) cc_final: 0.8104 (tp) REVERT: R 466 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.6765 (mtm110) REVERT: R 493 GLN cc_start: 0.8050 (tm-30) cc_final: 0.7368 (tm-30) outliers start: 28 outliers final: 24 residues processed: 109 average time/residue: 0.1742 time to fit residues: 22.5019 Evaluate side-chains 118 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 90 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 TRP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 392 PHE Chi-restraints excluded: chain R residue 393 THR Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 408 ARG Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 455 LEU Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 0.0770 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3345 Z= 0.259 Angle : 0.764 10.525 4548 Z= 0.389 Chirality : 0.048 0.214 487 Planarity : 0.006 0.080 581 Dihedral : 8.281 50.967 521 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.70 % Favored : 90.05 % Rotamer: Outliers : 7.71 % Allowed : 26.00 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.73 (0.38), residues: 402 helix: -3.77 (0.78), residues: 19 sheet: -2.54 (0.42), residues: 124 loop : -2.42 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP H 109 HIS 0.001 0.000 HIS L 34 PHE 0.010 0.001 PHE H 106 TYR 0.023 0.002 TYR H 105 ARG 0.005 0.001 ARG L 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 93 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: H 60 TYR cc_start: 0.8342 (m-80) cc_final: 0.7927 (m-10) REVERT: H 69 VAL cc_start: 0.8358 (t) cc_final: 0.7943 (t) REVERT: H 104 TRP cc_start: 0.8640 (m100) cc_final: 0.8409 (m100) REVERT: L 62 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.7365 (p90) REVERT: L 79 GLN cc_start: 0.8586 (mp10) cc_final: 0.7842 (mp10) REVERT: L 100 GLN cc_start: 0.7441 (tm-30) cc_final: 0.7214 (tm-30) REVERT: R 387 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8370 (tt) REVERT: R 408 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8287 (ptm-80) REVERT: R 418 ILE cc_start: 0.8360 (tp) cc_final: 0.7546 (tp) REVERT: R 466 ARG cc_start: 0.6996 (OUTLIER) cc_final: 0.6734 (mtm110) REVERT: R 493 GLN cc_start: 0.8056 (tm-30) cc_final: 0.7410 (tm-30) outliers start: 27 outliers final: 22 residues processed: 109 average time/residue: 0.1918 time to fit residues: 24.5256 Evaluate side-chains 117 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 91 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 TRP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 392 PHE Chi-restraints excluded: chain R residue 393 THR Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 408 ARG Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 22 optimal weight: 0.0980 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 0.0970 chunk 26 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 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 = 0.3944 r_free = 0.3944 target = 0.151445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.127496 restraints weight = 4917.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.130134 restraints weight = 3400.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.131966 restraints weight = 2640.482| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3345 Z= 0.208 Angle : 0.750 10.927 4548 Z= 0.381 Chirality : 0.048 0.191 487 Planarity : 0.006 0.080 581 Dihedral : 7.620 51.732 519 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.70 % Favored : 90.05 % Rotamer: Outliers : 6.86 % Allowed : 26.86 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.55 (0.38), residues: 402 helix: -3.79 (0.81), residues: 18 sheet: -2.43 (0.43), residues: 121 loop : -2.30 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP H 109 HIS 0.000 0.000 HIS L 34 PHE 0.010 0.001 PHE R 392 TYR 0.024 0.002 TYR R 453 ARG 0.005 0.001 ARG L 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1446.19 seconds wall clock time: 26 minutes 21.63 seconds (1581.63 seconds total)