Starting phenix.real_space_refine on Fri Aug 2 20:20:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw4_38730/08_2024/8xw4_38730.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw4_38730/08_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_38730/08_2024/8xw4_38730.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw4_38730/08_2024/8xw4_38730.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw4_38730/08_2024/8xw4_38730.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xw4_38730/08_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-5409/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: 3.49, 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: 1.90 Conformation dependent library (CDL) restraints added in 991.1 milliseconds 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: 0.43 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: 1.24 Time building geometry restraints manager: 2.10 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 3.120 nonbonded pdb=" OE1 GLN A 302 " pdb=" N VAL A 307 " model vdw 1.766 3.120 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 3.040 ... (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: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 17.720 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.800 ------------------------------------------------------------------------------- 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 : 0.543 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: 0.1582 time to fit residues: 24.5377 Evaluate side-chains 87 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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: 0.7980 chunk 46 optimal weight: 0.0970 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 31 optimal weight: 0.0970 chunk 24 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.0670 chunk 55 optimal weight: 7.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- 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 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: 0.7522 moved from start: 0.1547 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= 0.192 Angle : 0.690 8.759 7006 Z= 0.354 Chirality : 0.044 0.176 796 Planarity : 0.004 0.046 856 Dihedral : 5.548 31.080 669 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 2.90 % Allowed : 9.98 % Favored : 87.11 % 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: -0.41 (0.35), residues: 611 helix: 1.23 (0.27), residues: 379 sheet: -3.04 (1.23), residues: 12 loop : -2.95 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 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 0.004 0.000 ARG A 293 *********************** 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 125 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 244 ILE cc_start: 0.8852 (mm) cc_final: 0.8387 (tp) REVERT: A 260 PHE cc_start: 0.8522 (m-10) cc_final: 0.8102 (m-80) REVERT: A 361 MET cc_start: 0.7046 (mmp) cc_final: 0.6509 (mmp) REVERT: A 628 MET cc_start: 0.8023 (mmm) cc_final: 0.7753 (mmp) REVERT: A 683 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8320 (mt0) outliers start: 16 outliers final: 10 residues processed: 117 average time/residue: 0.1463 time to fit residues: 22.7089 Evaluate side-chains 99 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 207 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 450 THR 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 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: 4.9990 chunk 17 optimal weight: 20.0000 chunk 46 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 ** 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: 0.7556 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5165 Z= 0.204 Angle : 0.664 12.206 7006 Z= 0.337 Chirality : 0.043 0.139 796 Planarity : 0.004 0.050 856 Dihedral : 5.261 31.664 669 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 3.81 % Allowed : 13.43 % Favored : 82.76 % 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: -0.27 (0.35), residues: 611 helix: 1.37 (0.27), residues: 375 sheet: -2.21 (1.53), residues: 12 loop : -2.93 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 694 HIS 0.005 0.001 HIS A 656 PHE 0.018 0.001 PHE A 712 TYR 0.022 0.001 TYR A 336 ARG 0.003 0.000 ARG A 293 *********************** 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: 21 poor density : 96 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 ILE cc_start: 0.8873 (mm) cc_final: 0.8441 (tp) REVERT: A 361 MET cc_start: 0.6901 (mmp) cc_final: 0.6099 (mmp) REVERT: A 628 MET cc_start: 0.8167 (mmm) cc_final: 0.7949 (mmp) REVERT: A 683 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8364 (mt0) outliers start: 21 outliers final: 16 residues processed: 107 average time/residue: 0.1484 time to fit residues: 21.7430 Evaluate side-chains 100 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 83 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 207 LEU Chi-restraints excluded: chain A residue 292 GLU 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 488 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 640 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: 1.9990 chunk 28 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 29 optimal weight: 20.0000 chunk 52 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 49 optimal weight: 0.0050 overall best weight: 0.7200 ------------------------------------------------------------------------------- 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 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: 0.7533 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 5165 Z= 0.223 Angle : 0.671 12.150 7006 Z= 0.335 Chirality : 0.042 0.173 796 Planarity : 0.004 0.050 856 Dihedral : 5.127 30.003 669 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 3.27 % Allowed : 16.88 % Favored : 79.85 % 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: -0.13 (0.35), residues: 611 helix: 1.41 (0.27), residues: 378 sheet: -1.68 (1.62), residues: 12 loop : -2.82 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 694 HIS 0.005 0.001 HIS A 656 PHE 0.016 0.001 PHE A 52 TYR 0.020 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 116 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 197 ASN cc_start: 0.8484 (t0) cc_final: 0.7735 (t0) REVERT: A 244 ILE cc_start: 0.8856 (mm) cc_final: 0.8455 (tp) REVERT: A 260 PHE cc_start: 0.8508 (m-10) cc_final: 0.8027 (m-80) REVERT: A 298 PHE cc_start: 0.9029 (m-10) cc_final: 0.8813 (m-10) REVERT: A 338 LYS cc_start: 0.9347 (mmtp) cc_final: 0.8997 (pttt) REVERT: A 361 MET cc_start: 0.6699 (mmt) cc_final: 0.5653 (mmp) REVERT: A 628 MET cc_start: 0.8194 (mmm) cc_final: 0.7959 (mmp) REVERT: A 683 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8351 (mt0) outliers start: 18 outliers final: 15 residues processed: 105 average time/residue: 0.1337 time to fit residues: 19.7651 Evaluate side-chains 107 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 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 488 SER 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 709 THR 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: 8.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 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: 0.7624 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5165 Z= 0.305 Angle : 0.686 13.822 7006 Z= 0.352 Chirality : 0.045 0.184 796 Planarity : 0.004 0.049 856 Dihedral : 5.256 32.892 669 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 4.54 % Allowed : 17.79 % Favored : 77.68 % 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: -0.19 (0.35), residues: 611 helix: 1.41 (0.27), residues: 377 sheet: -1.90 (1.46), residues: 12 loop : -2.91 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 407 HIS 0.015 0.001 HIS A 150 PHE 0.018 0.002 PHE A 52 TYR 0.024 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 117 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 92 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 244 ILE cc_start: 0.8814 (mm) cc_final: 0.8275 (tp) REVERT: A 260 PHE cc_start: 0.8493 (m-10) cc_final: 0.8044 (m-80) REVERT: A 282 MET cc_start: 0.8388 (ptm) cc_final: 0.8177 (ptt) REVERT: A 349 ARG cc_start: 0.9022 (tpp80) cc_final: 0.8792 (tpp80) REVERT: A 361 MET cc_start: 0.6755 (mmt) cc_final: 0.5495 (mmp) REVERT: A 418 ILE cc_start: 0.6231 (OUTLIER) cc_final: 0.5614 (mt) REVERT: A 586 LEU cc_start: 0.8756 (tp) cc_final: 0.8480 (tp) REVERT: A 683 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8411 (mt0) outliers start: 25 outliers final: 19 residues processed: 106 average time/residue: 0.1323 time to fit residues: 20.0464 Evaluate side-chains 106 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 85 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 292 GLU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 418 ILE 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 476 THR Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 640 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 14 optimal weight: 30.0000 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 0.1980 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5165 Z= 0.205 Angle : 0.658 12.052 7006 Z= 0.332 Chirality : 0.043 0.202 796 Planarity : 0.004 0.048 856 Dihedral : 5.141 30.028 669 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 4.17 % Allowed : 19.60 % Favored : 76.23 % 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: -0.04 (0.35), residues: 611 helix: 1.52 (0.27), residues: 375 sheet: -1.70 (1.51), residues: 12 loop : -2.79 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP A 694 HIS 0.004 0.001 HIS A 656 PHE 0.021 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 124 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 101 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ASN cc_start: 0.8467 (t0) cc_final: 0.7744 (t0) REVERT: A 244 ILE cc_start: 0.8802 (mm) cc_final: 0.8342 (tp) REVERT: A 260 PHE cc_start: 0.8499 (m-10) cc_final: 0.8033 (m-80) REVERT: A 282 MET cc_start: 0.8260 (ptm) cc_final: 0.7793 (ptm) REVERT: A 349 ARG cc_start: 0.8996 (tpp80) cc_final: 0.8589 (tpp80) REVERT: A 361 MET cc_start: 0.6549 (mmt) cc_final: 0.5551 (mmp) REVERT: A 586 LEU cc_start: 0.8678 (tp) cc_final: 0.8396 (tp) REVERT: A 628 MET cc_start: 0.8110 (mmm) cc_final: 0.7758 (mmp) REVERT: A 683 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8327 (mt0) outliers start: 23 outliers final: 19 residues processed: 112 average time/residue: 0.1385 time to fit residues: 21.0004 Evaluate side-chains 111 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 207 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 364 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 476 THR Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 683 GLN 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: 0.9980 chunk 43 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 0.2980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 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: 0.7589 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5165 Z= 0.240 Angle : 0.677 14.310 7006 Z= 0.344 Chirality : 0.043 0.224 796 Planarity : 0.004 0.045 856 Dihedral : 5.095 30.787 669 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 4.36 % Allowed : 20.33 % Favored : 75.32 % 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: 0.00 (0.35), residues: 611 helix: 1.54 (0.27), residues: 375 sheet: -1.65 (1.50), residues: 12 loop : -2.76 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP A 694 HIS 0.008 0.001 HIS A 150 PHE 0.020 0.001 PHE A 52 TYR 0.022 0.001 TYR A 336 ARG 0.001 0.000 ARG A 156 *********************** 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 116 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ASN cc_start: 0.8431 (t0) cc_final: 0.7723 (t0) REVERT: A 244 ILE cc_start: 0.8821 (mm) cc_final: 0.8367 (tp) REVERT: A 260 PHE cc_start: 0.8504 (m-10) cc_final: 0.8045 (m-80) REVERT: A 282 MET cc_start: 0.8205 (ptm) cc_final: 0.7785 (ptm) REVERT: A 310 MET cc_start: 0.7646 (tpp) cc_final: 0.7445 (tpp) REVERT: A 349 ARG cc_start: 0.8998 (tpp80) cc_final: 0.8797 (tpp80) REVERT: A 361 MET cc_start: 0.6497 (mmt) cc_final: 0.5663 (mmp) REVERT: A 586 LEU cc_start: 0.8710 (tp) cc_final: 0.8438 (tp) REVERT: A 628 MET cc_start: 0.8187 (mmm) cc_final: 0.7843 (mmp) REVERT: A 683 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8314 (mt0) outliers start: 24 outliers final: 19 residues processed: 107 average time/residue: 0.1820 time to fit residues: 26.4561 Evaluate side-chains 111 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 364 VAL 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 476 THR Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 640 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 46 optimal weight: 0.0270 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 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: 0.2734 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= 0.191 Angle : 0.675 13.591 7006 Z= 0.336 Chirality : 0.043 0.200 796 Planarity : 0.004 0.044 856 Dihedral : 5.005 28.677 669 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 3.81 % Allowed : 20.87 % Favored : 75.32 % 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: 0.09 (0.35), residues: 611 helix: 1.60 (0.27), residues: 375 sheet: -1.56 (1.53), residues: 12 loop : -2.70 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 694 HIS 0.004 0.001 HIS A 403 PHE 0.024 0.001 PHE A 52 TYR 0.024 0.001 TYR A 232 ARG 0.003 0.000 ARG A 63 *********************** 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 126 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ASN cc_start: 0.8422 (t0) cc_final: 0.7684 (t0) REVERT: A 244 ILE cc_start: 0.8821 (mm) cc_final: 0.8394 (tp) REVERT: A 260 PHE cc_start: 0.8465 (m-10) cc_final: 0.8017 (m-80) REVERT: A 282 MET cc_start: 0.8134 (ptm) cc_final: 0.7692 (ptm) REVERT: A 361 MET cc_start: 0.6288 (mmt) cc_final: 0.5527 (mmp) REVERT: A 628 MET cc_start: 0.8161 (mmm) cc_final: 0.7903 (mmp) REVERT: A 683 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8313 (mt0) outliers start: 21 outliers final: 19 residues processed: 118 average time/residue: 0.1509 time to fit residues: 23.7300 Evaluate side-chains 120 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 364 VAL 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 476 THR Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 640 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 49 optimal weight: 0.0010 chunk 51 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- 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 329 GLN ** 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: 0.7534 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5165 Z= 0.200 Angle : 0.688 15.111 7006 Z= 0.345 Chirality : 0.043 0.255 796 Planarity : 0.004 0.042 856 Dihedral : 4.967 27.844 669 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % 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: 0.06 (0.35), residues: 611 helix: 1.42 (0.27), residues: 383 sheet: -1.51 (1.54), residues: 12 loop : -2.54 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP A 694 HIS 0.005 0.001 HIS A 656 PHE 0.024 0.001 PHE A 52 TYR 0.024 0.001 TYR A 336 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 121 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 99 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ASN cc_start: 0.8367 (t0) cc_final: 0.7637 (t0) REVERT: A 244 ILE cc_start: 0.8848 (mm) cc_final: 0.8437 (tp) REVERT: A 260 PHE cc_start: 0.8431 (m-10) cc_final: 0.8010 (m-80) REVERT: A 282 MET cc_start: 0.8030 (ptm) cc_final: 0.7626 (ptm) REVERT: A 338 LYS cc_start: 0.9470 (mmtp) cc_final: 0.9127 (pttt) REVERT: A 361 MET cc_start: 0.6315 (mmt) cc_final: 0.5613 (mmp) outliers start: 22 outliers final: 20 residues processed: 111 average time/residue: 0.1709 time to fit residues: 25.1877 Evaluate side-chains 115 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 364 VAL 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 476 THR Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 650 MET 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: 1.9990 chunk 5 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 0.0020 chunk 38 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 14 optimal weight: 0.0170 chunk 44 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 overall best weight: 0.5826 ------------------------------------------------------------------------------- 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 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: 0.7505 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5165 Z= 0.196 Angle : 0.710 15.317 7006 Z= 0.355 Chirality : 0.043 0.249 796 Planarity : 0.004 0.039 856 Dihedral : 4.885 26.806 669 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 3.45 % Allowed : 22.69 % Favored : 73.87 % 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: 0.13 (0.35), residues: 611 helix: 1.45 (0.26), residues: 384 sheet: -1.47 (1.56), residues: 12 loop : -2.47 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 694 HIS 0.005 0.001 HIS A 656 PHE 0.027 0.001 PHE A 52 TYR 0.022 0.001 TYR A 336 ARG 0.001 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 120 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ASN cc_start: 0.8334 (t0) cc_final: 0.7601 (t0) REVERT: A 244 ILE cc_start: 0.8815 (mm) cc_final: 0.8470 (tp) REVERT: A 260 PHE cc_start: 0.8474 (m-10) cc_final: 0.8108 (m-10) REVERT: A 282 MET cc_start: 0.7951 (ptm) cc_final: 0.7563 (ptm) REVERT: A 338 LYS cc_start: 0.9463 (mmtp) cc_final: 0.9140 (pttt) REVERT: A 361 MET cc_start: 0.6345 (mmt) cc_final: 0.5672 (mmp) outliers start: 19 outliers final: 16 residues processed: 111 average time/residue: 0.1547 time to fit residues: 22.9485 Evaluate side-chains 114 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 292 GLU 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 476 THR Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 650 MET 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: 0.9980 chunk 20 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 2 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.180133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.132599 restraints weight = 7360.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.133516 restraints weight = 4686.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.135586 restraints weight = 3297.577| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3200 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 : 0.753 15.444 7006 Z= 0.365 Chirality : 0.044 0.235 796 Planarity : 0.004 0.038 856 Dihedral : 4.886 26.607 669 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 3.81 % Allowed : 22.87 % 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: 0.18 (0.35), residues: 611 helix: 1.45 (0.27), residues: 384 sheet: -1.42 (1.54), residues: 12 loop : -2.38 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 694 HIS 0.005 0.001 HIS A 656 PHE 0.028 0.001 PHE A 545 TYR 0.025 0.002 TYR A 232 ARG 0.002 0.000 ARG A 280 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1448.78 seconds wall clock time: 26 minutes 38.74 seconds (1598.74 seconds total)