Starting phenix.real_space_refine on Fri Jul 19 00:17:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw4_38730/07_2024/8xw4_38730.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw4_38730/07_2024/8xw4_38730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw4_38730/07_2024/8xw4_38730.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw4_38730/07_2024/8xw4_38730.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw4_38730/07_2024/8xw4_38730.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw4_38730/07_2024/8xw4_38730.cif" } resolution = 3.84 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= 0.003 sd= 0.068 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 41 5.16 5 C 3331 2.51 5 N 810 2.21 5 O 845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 29": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 141": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A GLU 331": "OE1" <-> "OE2" Residue "A TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A GLU 421": "OE1" <-> "OE2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "A GLU 617": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 5027 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 5027 Classifications: {'peptide': 619} Link IDs: {'PTRANS': 24, 'TRANS': 594} Chain breaks: 3 Time building chain proxies: 3.48, per 1000 atoms: 0.69 Number of scatterers: 5027 At special positions: 0 Unit cell: (90.47, 94.62, 99.6, 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 41 16.00 O 845 8.00 N 810 7.00 C 3331 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: 1.94 Conformation dependent library (CDL) restraints added in 1.0 seconds 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1182 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 1 sheets defined 68.8% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 36 through 39 removed outlier: 3.558A pdb=" N GLY A 39 " --> pdb=" O LEU A 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 36 through 39' Processing helix chain 'A' and resid 40 through 67 removed outlier: 3.844A pdb=" N VAL A 44 " --> pdb=" O GLY A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 removed outlier: 3.861A pdb=" N CYS A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 180 removed outlier: 4.885A pdb=" N LEU A 174 " --> pdb=" O VAL A 170 " (cutoff:3.500A) Proline residue: A 175 - end of helix removed outlier: 3.690A pdb=" N GLY A 180 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 removed outlier: 3.779A pdb=" N ARG A 192 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 228 removed outlier: 3.949A pdb=" N LEU A 207 " --> pdb=" O ASN A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 Processing helix chain 'A' and resid 277 through 305 Processing helix chain 'A' and resid 331 through 355 Processing helix chain 'A' and resid 368 through 379 removed outlier: 3.619A pdb=" N PHE A 379 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 457 removed outlier: 4.175A pdb=" N CYS A 434 " --> pdb=" O TRP A 430 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 472 through 502 removed outlier: 4.203A pdb=" N PHE A 479 " --> pdb=" O ILE A 475 " (cutoff:3.500A) Proline residue: A 480 - end of helix Proline residue: A 492 - end of helix Processing helix chain 'A' and resid 506 through 527 Processing helix chain 'A' and resid 527 through 549 Processing helix chain 'A' and resid 556 through 560 removed outlier: 3.667A pdb=" N CYS A 559 " --> pdb=" O ARG A 556 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 560 " --> pdb=" O PHE A 557 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 556 through 560' Processing helix chain 'A' and resid 562 through 566 removed outlier: 3.780A pdb=" N GLY A 566 " --> pdb=" O PRO A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 586 removed outlier: 4.099A pdb=" N MET A 583 " --> pdb=" O ILE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 595 removed outlier: 5.814A pdb=" N MET A 593 " --> pdb=" O PRO A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 637 removed outlier: 3.762A pdb=" N ALA A 623 " --> pdb=" O GLN A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 667 removed outlier: 4.584A pdb=" N PHE A 647 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR A 667 " --> pdb=" O LEU A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 704 removed outlier: 3.918A pdb=" N SER A 678 " --> pdb=" O LYS A 674 " (cutoff:3.500A) Proline residue: A 688 - end of helix Processing helix chain 'A' and resid 707 through 730 removed outlier: 3.587A pdb=" N HIS A 727 " --> pdb=" O ILE A 723 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL A 728 " --> pdb=" O CYS A 724 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N CYS A 729 " --> pdb=" O LEU A 725 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 241 through 243 309 hydrogen bonds defined for protein. 918 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 2.15 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: 1263 1.33 - 1.45: 1024 1.45 - 1.57: 2818 1.57 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 5165 Sorted by residual: bond pdb=" CB TRP A 694 " pdb=" CG TRP A 694 " ideal model delta sigma weight residual 1.498 1.449 0.049 3.10e-02 1.04e+03 2.47e+00 bond pdb=" CB MET A 628 " pdb=" CG MET A 628 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.33e+00 bond pdb=" CB LEU A 445 " pdb=" CG LEU A 445 " ideal model delta sigma weight residual 1.530 1.501 0.029 2.00e-02 2.50e+03 2.04e+00 bond pdb=" CB GLN A 155 " pdb=" CG GLN A 155 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.92e+00 bond pdb=" C ILE A 588 " pdb=" N PRO A 589 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.88e+00 ... (remaining 5160 not shown) Histogram of bond angle deviations from ideal: 97.92 - 105.15: 90 105.15 - 112.38: 2633 112.38 - 119.61: 1706 119.61 - 126.84: 2502 126.84 - 134.07: 75 Bond angle restraints: 7006 Sorted by residual: angle pdb=" C ILE A 425 " pdb=" N ARG A 426 " pdb=" CA ARG A 426 " ideal model delta sigma weight residual 120.89 128.04 -7.15 1.50e+00 4.44e-01 2.27e+01 angle pdb=" CA MET A 361 " pdb=" CB MET A 361 " pdb=" CG MET A 361 " ideal model delta sigma weight residual 114.10 121.64 -7.54 2.00e+00 2.50e-01 1.42e+01 angle pdb=" CB MET A 628 " pdb=" CG MET A 628 " pdb=" SD MET A 628 " ideal model delta sigma weight residual 112.70 102.19 10.51 3.00e+00 1.11e-01 1.23e+01 angle pdb=" N ILE A 689 " pdb=" CA ILE A 689 " pdb=" C ILE A 689 " ideal model delta sigma weight residual 110.72 107.20 3.52 1.01e+00 9.80e-01 1.21e+01 angle pdb=" C THR A 457 " pdb=" N MET A 458 " pdb=" CA MET A 458 " ideal model delta sigma weight residual 121.64 114.49 7.15 2.13e+00 2.20e-01 1.13e+01 ... (remaining 7001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 2673 16.68 - 33.35: 260 33.35 - 50.03: 78 50.03 - 66.70: 5 66.70 - 83.38: 5 Dihedral angle restraints: 3021 sinusoidal: 1195 harmonic: 1826 Sorted by residual: dihedral pdb=" CA ALA A 412 " pdb=" C ALA A 412 " pdb=" N PRO A 413 " pdb=" CA PRO A 413 " ideal model delta harmonic sigma weight residual 180.00 -143.48 -36.52 0 5.00e+00 4.00e-02 5.33e+01 dihedral pdb=" CA MET A 282 " pdb=" C MET A 282 " pdb=" N PHE A 283 " pdb=" CA PHE A 283 " ideal model delta harmonic sigma weight residual 180.00 155.61 24.39 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA GLU A 184 " pdb=" C GLU A 184 " pdb=" N ASN A 185 " pdb=" CA ASN A 185 " ideal model delta harmonic sigma weight residual 180.00 -156.60 -23.40 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 3018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 530 0.042 - 0.084: 183 0.084 - 0.125: 63 0.125 - 0.167: 12 0.167 - 0.209: 8 Chirality restraints: 796 Sorted by residual: chirality pdb=" CA MET A 223 " pdb=" N MET A 223 " pdb=" C MET A 223 " pdb=" CB MET A 223 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA TRP A 694 " pdb=" N TRP A 694 " pdb=" C TRP A 694 " pdb=" CB TRP A 694 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE A 474 " pdb=" CA ILE A 474 " pdb=" CG1 ILE A 474 " pdb=" CG2 ILE A 474 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.60e-01 ... (remaining 793 not shown) Planarity restraints: 856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 694 " -0.034 2.00e-02 2.50e+03 2.55e-02 1.62e+01 pdb=" CG TRP A 694 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP A 694 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 694 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 694 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 694 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 694 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 694 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 694 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 694 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 407 " 0.027 2.00e-02 2.50e+03 2.17e-02 1.17e+01 pdb=" CG TRP A 407 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP A 407 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 407 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 407 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 407 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 407 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 407 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 407 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 407 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 197 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.34e+00 pdb=" C ASN A 197 " -0.036 2.00e-02 2.50e+03 pdb=" O ASN A 197 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 198 " 0.012 2.00e-02 2.50e+03 ... (remaining 853 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 12 2.38 - 3.01: 3029 3.01 - 3.64: 7579 3.64 - 4.27: 10504 4.27 - 4.90: 17189 Nonbonded interactions: 38313 Sorted by model distance: nonbonded pdb=" NE2 GLN A 302 " pdb=" O VAL A 307 " model vdw 1.751 2.520 nonbonded pdb=" OE1 GLN A 302 " pdb=" N VAL A 307 " model vdw 1.766 2.520 nonbonded pdb=" OE1 GLN A 302 " pdb=" C ASN A 306 " model vdw 2.056 3.270 nonbonded pdb=" NE2 GLN A 302 " pdb=" C VAL A 307 " model vdw 2.084 3.350 nonbonded pdb=" O LYS A 675 " pdb=" OG SER A 678 " model vdw 2.252 2.440 ... (remaining 38308 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.150 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 : 0.006 0.049 5165 Z= 0.389 Angle : 0.871 10.510 7006 Z= 0.481 Chirality : 0.051 0.209 796 Planarity : 0.005 0.041 856 Dihedral : 14.645 83.378 1839 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.80 % Favored : 89.20 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: -0.84 (0.34), residues: 611 helix: 0.88 (0.27), residues: 385 sheet: -4.00 (0.92), residues: 12 loop : -3.15 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.004 TRP A 694 HIS 0.007 0.001 HIS A 656 PHE 0.025 0.002 PHE A 705 TYR 0.028 0.002 TYR A 297 ARG 0.003 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 244 ILE cc_start: 0.8804 (mm) cc_final: 0.8210 (tp) REVERT: A 260 PHE cc_start: 0.8500 (m-10) cc_final: 0.8070 (m-80) REVERT: A 292 GLU cc_start: 0.8936 (mp0) cc_final: 0.8562 (mp0) REVERT: A 298 PHE cc_start: 0.9058 (m-10) cc_final: 0.8722 (m-10) REVERT: A 349 ARG cc_start: 0.8845 (mmm-85) cc_final: 0.8610 (tpp80) REVERT: A 361 MET cc_start: 0.7502 (mmp) cc_final: 0.6983 (mmp) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1580 time to fit residues: 24.5505 Evaluate side-chains 87 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 0.1980 chunk 55 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5165 Z= 0.210 Angle : 0.691 8.548 7006 Z= 0.354 Chirality : 0.044 0.178 796 Planarity : 0.004 0.047 856 Dihedral : 5.607 32.114 669 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 3.45 % Allowed : 9.98 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: -0.42 (0.35), residues: 611 helix: 1.18 (0.27), residues: 386 sheet: -3.00 (1.22), residues: 12 loop : -3.01 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 694 HIS 0.005 0.001 HIS A 403 PHE 0.022 0.001 PHE A 712 TYR 0.019 0.002 TYR A 336 ARG 0.003 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 105 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: A 244 ILE cc_start: 0.8848 (mm) cc_final: 0.8370 (tp) REVERT: A 260 PHE cc_start: 0.8537 (m-10) cc_final: 0.8137 (m-80) REVERT: A 282 MET cc_start: 0.8495 (ptt) cc_final: 0.8288 (ptm) REVERT: A 298 PHE cc_start: 0.9144 (m-10) cc_final: 0.8867 (m-10) REVERT: A 361 MET cc_start: 0.7104 (mmp) cc_final: 0.6505 (mmp) REVERT: A 628 MET cc_start: 0.8087 (mmm) cc_final: 0.7792 (mmp) REVERT: A 683 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8332 (mt0) outliers start: 19 outliers final: 13 residues processed: 112 average time/residue: 0.1687 time to fit residues: 25.0339 Evaluate side-chains 103 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 683 GLN Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 725 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5165 Z= 0.272 Angle : 0.686 10.497 7006 Z= 0.352 Chirality : 0.044 0.174 796 Planarity : 0.005 0.049 856 Dihedral : 5.482 33.305 669 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 3.99 % Allowed : 14.34 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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 (0.35), residues: 611 helix: 1.23 (0.27), residues: 382 sheet: -2.30 (1.51), residues: 12 loop : -2.93 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 694 HIS 0.006 0.001 HIS A 656 PHE 0.018 0.002 PHE A 712 TYR 0.022 0.002 TYR A 336 ARG 0.003 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 244 ILE cc_start: 0.8872 (mm) cc_final: 0.8415 (tp) REVERT: A 260 PHE cc_start: 0.8525 (m-10) cc_final: 0.8031 (m-80) REVERT: A 298 PHE cc_start: 0.9152 (m-10) cc_final: 0.8892 (m-10) REVERT: A 361 MET cc_start: 0.6848 (mmp) cc_final: 0.6187 (mmp) REVERT: A 683 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8405 (mt0) outliers start: 22 outliers final: 17 residues processed: 107 average time/residue: 0.1286 time to fit residues: 19.1113 Evaluate side-chains 101 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 683 GLN Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 725 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 0.9980 chunk 28 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 0.0970 chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 29 optimal weight: 30.0000 chunk 52 optimal weight: 0.5980 chunk 15 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 HIS ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5165 Z= 0.194 Angle : 0.639 10.265 7006 Z= 0.326 Chirality : 0.043 0.180 796 Planarity : 0.004 0.047 856 Dihedral : 5.266 30.020 669 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 2.54 % Allowed : 18.69 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: -0.12 (0.35), residues: 611 helix: 1.44 (0.27), residues: 382 sheet: -1.44 (1.81), residues: 12 loop : -2.93 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 694 HIS 0.005 0.001 HIS A 403 PHE 0.017 0.001 PHE A 52 TYR 0.025 0.001 TYR A 336 ARG 0.002 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 0.581 Fit side-chains REVERT: A 197 ASN cc_start: 0.8468 (t0) cc_final: 0.7723 (t0) REVERT: A 244 ILE cc_start: 0.8848 (mm) cc_final: 0.8405 (tp) REVERT: A 260 PHE cc_start: 0.8472 (m-10) cc_final: 0.8010 (m-80) REVERT: A 298 PHE cc_start: 0.9081 (m-10) cc_final: 0.8862 (m-10) REVERT: A 338 LYS cc_start: 0.9389 (mmtp) cc_final: 0.9018 (pttt) REVERT: A 349 ARG cc_start: 0.8984 (tpp80) cc_final: 0.8761 (tpp80) REVERT: A 361 MET cc_start: 0.6558 (mmp) cc_final: 0.5588 (mmp) REVERT: A 683 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8346 (mt0) outliers start: 14 outliers final: 12 residues processed: 103 average time/residue: 0.1462 time to fit residues: 20.3111 Evaluate side-chains 103 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 683 GLN Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 725 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 50 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 HIS ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5165 Z= 0.277 Angle : 0.665 8.548 7006 Z= 0.343 Chirality : 0.044 0.189 796 Planarity : 0.004 0.046 856 Dihedral : 5.318 32.493 669 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 3.81 % Allowed : 19.24 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: -0.23 (0.35), residues: 611 helix: 1.30 (0.27), residues: 382 sheet: -1.23 (1.77), residues: 12 loop : -2.88 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 694 HIS 0.006 0.001 HIS A 656 PHE 0.018 0.001 PHE A 52 TYR 0.022 0.002 TYR A 336 ARG 0.002 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 0.595 Fit side-chains REVERT: A 197 ASN cc_start: 0.8446 (t0) cc_final: 0.7694 (t0) REVERT: A 244 ILE cc_start: 0.8821 (mm) cc_final: 0.8259 (tp) REVERT: A 260 PHE cc_start: 0.8456 (m-10) cc_final: 0.7980 (m-80) REVERT: A 298 PHE cc_start: 0.9106 (m-10) cc_final: 0.8879 (m-10) REVERT: A 349 ARG cc_start: 0.9001 (tpp80) cc_final: 0.8592 (tpp80) REVERT: A 361 MET cc_start: 0.6476 (mmt) cc_final: 0.5318 (mmp) outliers start: 21 outliers final: 16 residues processed: 104 average time/residue: 0.1471 time to fit residues: 21.2524 Evaluate side-chains 106 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 725 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.1980 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 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 150 HIS ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5165 Z= 0.182 Angle : 0.662 12.102 7006 Z= 0.329 Chirality : 0.042 0.191 796 Planarity : 0.004 0.044 856 Dihedral : 5.147 28.594 669 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 3.81 % Allowed : 20.33 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.35), residues: 611 helix: 1.33 (0.27), residues: 383 sheet: -1.20 (1.72), residues: 12 loop : -2.73 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 694 HIS 0.012 0.001 HIS A 150 PHE 0.020 0.001 PHE A 52 TYR 0.023 0.001 TYR A 336 ARG 0.002 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 100 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 197 ASN cc_start: 0.8357 (t0) cc_final: 0.7614 (t0) REVERT: A 244 ILE cc_start: 0.8808 (mm) cc_final: 0.8260 (tp) REVERT: A 260 PHE cc_start: 0.8495 (m-10) cc_final: 0.8030 (m-80) REVERT: A 298 PHE cc_start: 0.9090 (m-10) cc_final: 0.8807 (m-10) REVERT: A 361 MET cc_start: 0.6370 (mmt) cc_final: 0.5358 (mmp) REVERT: A 418 ILE cc_start: 0.5713 (OUTLIER) cc_final: 0.5504 (mm) REVERT: A 586 LEU cc_start: 0.8676 (tp) cc_final: 0.8370 (tp) outliers start: 21 outliers final: 17 residues processed: 111 average time/residue: 0.1361 time to fit residues: 20.5498 Evaluate side-chains 107 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 725 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 32 optimal weight: 0.3980 chunk 58 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 0.0470 chunk 11 optimal weight: 1.9990 overall best weight: 1.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 HIS ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5165 Z= 0.224 Angle : 0.663 8.066 7006 Z= 0.338 Chirality : 0.043 0.239 796 Planarity : 0.004 0.044 856 Dihedral : 5.120 29.676 669 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 4.36 % Allowed : 20.15 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.35), residues: 611 helix: 1.38 (0.27), residues: 383 sheet: -1.24 (1.63), residues: 12 loop : -2.68 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 694 HIS 0.009 0.001 HIS A 150 PHE 0.021 0.001 PHE A 52 TYR 0.023 0.001 TYR A 336 ARG 0.003 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ASN cc_start: 0.8362 (t0) cc_final: 0.7611 (t0) REVERT: A 244 ILE cc_start: 0.8813 (mm) cc_final: 0.8544 (tp) REVERT: A 260 PHE cc_start: 0.8426 (m-10) cc_final: 0.7978 (m-80) REVERT: A 338 LYS cc_start: 0.9474 (mmtp) cc_final: 0.9150 (pttt) REVERT: A 586 LEU cc_start: 0.8687 (tp) cc_final: 0.8399 (tp) outliers start: 24 outliers final: 16 residues processed: 113 average time/residue: 0.1415 time to fit residues: 21.5881 Evaluate side-chains 109 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 725 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.0070 chunk 5 optimal weight: 9.9990 chunk 46 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 HIS ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5165 Z= 0.201 Angle : 0.699 10.851 7006 Z= 0.350 Chirality : 0.045 0.240 796 Planarity : 0.004 0.043 856 Dihedral : 5.080 27.960 669 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 3.99 % Allowed : 21.42 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.35), residues: 611 helix: 1.34 (0.27), residues: 381 sheet: -1.19 (1.60), residues: 12 loop : -2.56 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 694 HIS 0.014 0.001 HIS A 150 PHE 0.024 0.001 PHE A 52 TYR 0.022 0.001 TYR A 336 ARG 0.004 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 97 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.7579 (OUTLIER) cc_final: 0.7235 (m) REVERT: A 197 ASN cc_start: 0.8335 (t0) cc_final: 0.7584 (t0) REVERT: A 244 ILE cc_start: 0.8803 (mm) cc_final: 0.8509 (tp) REVERT: A 260 PHE cc_start: 0.8514 (m-10) cc_final: 0.8052 (m-80) REVERT: A 338 LYS cc_start: 0.9475 (mmtp) cc_final: 0.9143 (pttt) REVERT: A 361 MET cc_start: 0.6047 (mmp) cc_final: 0.5545 (mmp) REVERT: A 586 LEU cc_start: 0.8682 (tp) cc_final: 0.8398 (tp) outliers start: 22 outliers final: 18 residues processed: 111 average time/residue: 0.1580 time to fit residues: 23.7800 Evaluate side-chains 113 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 94 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 725 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 49 optimal weight: 0.0770 chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 0.0000 chunk 57 optimal weight: 0.7980 chunk 27 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 HIS ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5165 Z= 0.206 Angle : 0.708 9.992 7006 Z= 0.351 Chirality : 0.045 0.272 796 Planarity : 0.004 0.038 856 Dihedral : 5.018 27.419 669 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.81 % Allowed : 21.23 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.35), residues: 611 helix: 1.42 (0.26), residues: 381 sheet: -1.08 (1.58), residues: 12 loop : -2.49 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 694 HIS 0.012 0.001 HIS A 150 PHE 0.026 0.001 PHE A 52 TYR 0.024 0.002 TYR A 232 ARG 0.003 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.7461 (OUTLIER) cc_final: 0.7108 (m) REVERT: A 197 ASN cc_start: 0.8321 (t0) cc_final: 0.7557 (t0) REVERT: A 243 PHE cc_start: 0.7774 (t80) cc_final: 0.7535 (t80) REVERT: A 244 ILE cc_start: 0.8801 (mm) cc_final: 0.8546 (tp) REVERT: A 260 PHE cc_start: 0.8515 (m-10) cc_final: 0.8058 (m-80) REVERT: A 338 LYS cc_start: 0.9463 (mmtp) cc_final: 0.9135 (pttt) REVERT: A 361 MET cc_start: 0.5880 (mmp) cc_final: 0.5421 (mmp) REVERT: A 628 MET cc_start: 0.7924 (mmm) cc_final: 0.7556 (mmp) outliers start: 21 outliers final: 18 residues processed: 116 average time/residue: 0.1400 time to fit residues: 21.9162 Evaluate side-chains 115 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 683 GLN Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 725 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 51 optimal weight: 0.3980 chunk 14 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 HIS ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5165 Z= 0.226 Angle : 0.739 11.927 7006 Z= 0.365 Chirality : 0.045 0.257 796 Planarity : 0.004 0.037 856 Dihedral : 5.060 27.417 669 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.63 % Allowed : 23.05 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.35), residues: 611 helix: 1.48 (0.27), residues: 382 sheet: -0.97 (1.54), residues: 12 loop : -2.48 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP A 694 HIS 0.011 0.001 HIS A 150 PHE 0.027 0.002 PHE A 52 TYR 0.022 0.002 TYR A 336 ARG 0.002 0.000 ARG A 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.7461 (OUTLIER) cc_final: 0.7111 (m) REVERT: A 197 ASN cc_start: 0.8350 (t0) cc_final: 0.7594 (t0) REVERT: A 243 PHE cc_start: 0.7722 (t80) cc_final: 0.7454 (t80) REVERT: A 244 ILE cc_start: 0.8818 (mm) cc_final: 0.8569 (tp) REVERT: A 260 PHE cc_start: 0.8508 (m-10) cc_final: 0.8049 (m-80) REVERT: A 338 LYS cc_start: 0.9461 (mmtp) cc_final: 0.9110 (pttt) REVERT: A 361 MET cc_start: 0.5893 (mmp) cc_final: 0.5381 (mmp) REVERT: A 557 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.8415 (m-10) REVERT: A 628 MET cc_start: 0.8091 (mmm) cc_final: 0.7776 (mmp) outliers start: 20 outliers final: 17 residues processed: 111 average time/residue: 0.1651 time to fit residues: 24.4102 Evaluate side-chains 113 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 94 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 557 PHE Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 725 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.180755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.133177 restraints weight = 7313.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.134577 restraints weight = 4828.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.136529 restraints weight = 3380.182| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5165 Z= 0.208 Angle : 0.736 11.632 7006 Z= 0.363 Chirality : 0.045 0.243 796 Planarity : 0.004 0.036 856 Dihedral : 5.043 27.144 669 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 3.63 % Allowed : 23.23 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.35), residues: 611 helix: 1.67 (0.27), residues: 374 sheet: -0.86 (1.53), residues: 12 loop : -2.62 (0.40), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP A 694 HIS 0.005 0.001 HIS A 656 PHE 0.027 0.001 PHE A 52 TYR 0.021 0.002 TYR A 336 ARG 0.002 0.000 ARG A 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1439.47 seconds wall clock time: 26 minutes 27.55 seconds (1587.55 seconds total)