Starting phenix.real_space_refine on Sun Mar 10 21:15:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grs_34214/03_2024/8grs_34214_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grs_34214/03_2024/8grs_34214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grs_34214/03_2024/8grs_34214.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grs_34214/03_2024/8grs_34214.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grs_34214/03_2024/8grs_34214_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grs_34214/03_2024/8grs_34214_neut_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 31 5.16 5 C 3411 2.51 5 N 821 2.21 5 O 884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 18": "NH1" <-> "NH2" Residue "A GLU 19": "OE1" <-> "OE2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 73": "NH1" <-> "NH2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ASP 191": "OD1" <-> "OD2" Residue "A GLU 242": "OE1" <-> "OE2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A ASP 250": "OD1" <-> "OD2" Residue "A ASP 259": "OD1" <-> "OD2" Residue "A TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A ARG 334": "NH1" <-> "NH2" Residue "A GLU 337": "OE1" <-> "OE2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A ARG 417": "NH1" <-> "NH2" Residue "A PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 447": "OD1" <-> "OD2" Residue "A GLU 498": "OE1" <-> "OE2" Residue "A ASP 526": "OD1" <-> "OD2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A GLU 545": "OE1" <-> "OE2" Residue "A ARG 574": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A ARG 595": "NH1" <-> "NH2" Residue "A GLU 660": "OE1" <-> "OE2" Residue "A PHE 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 689": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5148 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 5148 Unusual residues: {'POV': 1} Classifications: {'peptide': 626, 'undetermined': 1} Link IDs: {'PTRANS': 22, 'TRANS': 603, None: 1} Not linked: pdbres="GLY A 718 " pdbres="POV A 901 " Chain breaks: 4 Time building chain proxies: 3.40, per 1000 atoms: 0.66 Number of scatterers: 5148 At special positions: 0 Unit cell: (95.12, 82.82, 86.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 P 1 15.00 O 884 8.00 N 821 7.00 C 3411 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: 1.99 Conformation dependent library (CDL) restraints added in 942.1 milliseconds 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1198 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 0 sheets defined 59.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 13 through 19 removed outlier: 3.662A pdb=" N ARG A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 66 removed outlier: 4.156A pdb=" N LEU A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 166 Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 191 through 216 removed outlier: 3.694A pdb=" N HIS A 196 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 201 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 210 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS A 213 " --> pdb=" O PHE A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 251 No H-bonds generated for 'chain 'A' and resid 248 through 251' Processing helix chain 'A' and resid 269 through 288 removed outlier: 4.338A pdb=" N ASN A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 349 removed outlier: 4.035A pdb=" N LYS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASP A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLU A 339 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Proline residue: A 346 - end of helix Processing helix chain 'A' and resid 364 through 371 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 415 through 445 Proline residue: A 439 - end of helix Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 467 through 490 removed outlier: 3.799A pdb=" N LEU A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) Proline residue: A 480 - end of helix Processing helix chain 'A' and resid 495 through 533 Proline residue: A 518 - end of helix Processing helix chain 'A' and resid 554 through 573 Processing helix chain 'A' and resid 575 through 586 removed outlier: 6.160A pdb=" N LEU A 580 " --> pdb=" O PRO A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 598 Processing helix chain 'A' and resid 609 through 627 removed outlier: 4.121A pdb=" N ILE A 626 " --> pdb=" O VAL A 622 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N THR A 627 " --> pdb=" O ALA A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 631 No H-bonds generated for 'chain 'A' and resid 629 through 631' Processing helix chain 'A' and resid 633 through 649 removed outlier: 3.554A pdb=" N ILE A 637 " --> pdb=" O PRO A 633 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N TYR A 638 " --> pdb=" O PHE A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 688 removed outlier: 3.571A pdb=" N PHE A 665 " --> pdb=" O LYS A 661 " (cutoff:3.500A) Proline residue: A 675 - end of helix Processing helix chain 'A' and resid 695 through 716 255 hydrogen bonds defined for protein. 708 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: 1.31 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 763 1.27 - 1.41: 1434 1.41 - 1.54: 3010 1.54 - 1.67: 30 1.67 - 1.81: 46 Bond restraints: 5283 Sorted by residual: bond pdb=" CA ILE A 511 " pdb=" C ILE A 511 " ideal model delta sigma weight residual 1.524 1.399 0.126 1.16e-02 7.43e+03 1.17e+02 bond pdb=" C VAL A 153 " pdb=" O VAL A 153 " ideal model delta sigma weight residual 1.236 1.138 0.099 1.11e-02 8.12e+03 7.94e+01 bond pdb=" CA ALA A 562 " pdb=" C ALA A 562 " ideal model delta sigma weight residual 1.524 1.416 0.108 1.28e-02 6.10e+03 7.12e+01 bond pdb=" CA SER A 157 " pdb=" C SER A 157 " ideal model delta sigma weight residual 1.523 1.416 0.107 1.34e-02 5.57e+03 6.35e+01 bond pdb=" CA PHE A 512 " pdb=" C PHE A 512 " ideal model delta sigma weight residual 1.523 1.418 0.105 1.34e-02 5.57e+03 6.18e+01 ... (remaining 5278 not shown) Histogram of bond angle deviations from ideal: 93.35 - 101.58: 42 101.58 - 109.81: 1073 109.81 - 118.04: 2884 118.04 - 126.27: 3076 126.27 - 134.51: 88 Bond angle restraints: 7163 Sorted by residual: angle pdb=" C ILE A 511 " pdb=" CA ILE A 511 " pdb=" CB ILE A 511 " ideal model delta sigma weight residual 111.70 93.35 18.35 1.28e+00 6.10e-01 2.06e+02 angle pdb=" N ILE A 511 " pdb=" CA ILE A 511 " pdb=" C ILE A 511 " ideal model delta sigma weight residual 110.23 96.00 14.23 1.04e+00 9.25e-01 1.87e+02 angle pdb=" N GLU A 134 " pdb=" CA GLU A 134 " pdb=" C GLU A 134 " ideal model delta sigma weight residual 114.56 97.71 16.85 1.27e+00 6.20e-01 1.76e+02 angle pdb=" C LEU A 517 " pdb=" N PRO A 518 " pdb=" CA PRO A 518 " ideal model delta sigma weight residual 119.05 105.94 13.11 1.11e+00 8.12e-01 1.40e+02 angle pdb=" C ALA A 674 " pdb=" N PRO A 675 " pdb=" CA PRO A 675 " ideal model delta sigma weight residual 119.32 106.81 12.51 1.14e+00 7.69e-01 1.21e+02 ... (remaining 7158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.14: 2419 21.14 - 42.27: 374 42.27 - 63.41: 283 63.41 - 84.54: 15 84.54 - 105.68: 5 Dihedral angle restraints: 3096 sinusoidal: 1249 harmonic: 1847 Sorted by residual: dihedral pdb=" C ILE A 511 " pdb=" N ILE A 511 " pdb=" CA ILE A 511 " pdb=" CB ILE A 511 " ideal model delta harmonic sigma weight residual -122.00 -97.70 -24.30 0 2.50e+00 1.60e-01 9.45e+01 dihedral pdb=" C VAL A 244 " pdb=" N VAL A 244 " pdb=" CA VAL A 244 " pdb=" CB VAL A 244 " ideal model delta harmonic sigma weight residual -122.00 -134.63 12.63 0 2.50e+00 1.60e-01 2.55e+01 dihedral pdb=" C ILE A 183 " pdb=" N ILE A 183 " pdb=" CA ILE A 183 " pdb=" CB ILE A 183 " ideal model delta harmonic sigma weight residual -122.00 -133.65 11.65 0 2.50e+00 1.60e-01 2.17e+01 ... (remaining 3093 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.111: 572 0.111 - 0.222: 176 0.222 - 0.333: 44 0.333 - 0.443: 16 0.443 - 0.554: 7 Chirality restraints: 815 Sorted by residual: chirality pdb=" CG LEU A 331 " pdb=" CB LEU A 331 " pdb=" CD1 LEU A 331 " pdb=" CD2 LEU A 331 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.67e+00 chirality pdb=" CA LEU A 517 " pdb=" N LEU A 517 " pdb=" C LEU A 517 " pdb=" CB LEU A 517 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.67e+00 chirality pdb=" CA ALA A 267 " pdb=" N ALA A 267 " pdb=" C ALA A 267 " pdb=" CB ALA A 267 " both_signs ideal model delta sigma weight residual False 2.48 2.01 0.47 2.00e-01 2.50e+01 5.60e+00 ... (remaining 812 not shown) Planarity restraints: 869 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 517 " 0.132 5.00e-02 4.00e+02 2.01e-01 6.48e+01 pdb=" N PRO A 518 " -0.348 5.00e-02 4.00e+02 pdb=" CA PRO A 518 " 0.101 5.00e-02 4.00e+02 pdb=" CD PRO A 518 " 0.115 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 162 " 0.120 5.00e-02 4.00e+02 1.78e-01 5.06e+01 pdb=" N PRO A 163 " -0.307 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " 0.083 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " 0.103 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 674 " 0.117 5.00e-02 4.00e+02 1.70e-01 4.63e+01 pdb=" N PRO A 675 " -0.293 5.00e-02 4.00e+02 pdb=" CA PRO A 675 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO A 675 " 0.102 5.00e-02 4.00e+02 ... (remaining 866 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.01: 2 2.01 - 2.73: 1139 2.73 - 3.45: 7288 3.45 - 4.18: 13516 4.18 - 4.90: 21986 Nonbonded interactions: 43931 Sorted by model distance: nonbonded pdb=" NH2 ARG A 249 " pdb=" OH TYR A 264 " model vdw 1.285 2.520 nonbonded pdb=" OG1 THR A 284 " pdb=" CB LEU A 331 " model vdw 1.475 3.440 nonbonded pdb=" OG1 THR A 284 " pdb=" CA LEU A 331 " model vdw 2.012 3.470 nonbonded pdb=" O PHE A 512 " pdb=" O MET A 513 " model vdw 2.265 3.040 nonbonded pdb=" N GLU A 134 " pdb=" N ASP A 135 " model vdw 2.273 2.560 ... (remaining 43926 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.080 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.570 Find NCS groups from input model: 0.140 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 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 : 0.016 0.128 5283 Z= 1.033 Angle : 1.944 18.350 7163 Z= 1.326 Chirality : 0.128 0.554 815 Planarity : 0.015 0.201 869 Dihedral : 26.307 105.676 1898 Min Nonbonded Distance : 1.285 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 5.84 % Allowed : 21.27 % Favored : 72.89 % Rotamer: Outliers : 44.03 % Allowed : 14.44 % Favored : 41.53 % Cbeta Deviations : 1.00 % 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: -5.46 (0.26), residues: 616 helix: -2.81 (0.20), residues: 384 sheet: -5.55 (0.90), residues: 15 loop : -4.85 (0.34), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 76 HIS 0.003 0.001 HIS A 145 PHE 0.017 0.002 PHE A 565 TYR 0.016 0.002 TYR A 139 ARG 0.009 0.001 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 177 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7527 (mtm-85) REVERT: A 55 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7724 (tp) REVERT: A 212 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6715 (mtt-85) REVERT: A 224 ASN cc_start: 0.4898 (OUTLIER) cc_final: 0.4357 (m-40) REVERT: A 277 LYS cc_start: 0.6149 (OUTLIER) cc_final: 0.5314 (tmtt) REVERT: A 429 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6665 (mm) REVERT: A 583 PHE cc_start: 0.7005 (OUTLIER) cc_final: 0.6740 (t80) REVERT: A 702 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7787 (tp) outliers start: 247 outliers final: 82 residues processed: 334 average time/residue: 0.2123 time to fit residues: 86.2427 Evaluate side-chains 226 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 136 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 212 ARG Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 435 PHE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 PRO Chi-restraints excluded: chain A residue 531 TRP Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 541 SER Chi-restraints excluded: chain A residue 543 ARG Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 644 MET Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 675 PRO Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 712 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 HIS ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 GLN ** A 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 5283 Z= 0.322 Angle : 0.857 11.022 7163 Z= 0.441 Chirality : 0.047 0.169 815 Planarity : 0.008 0.084 869 Dihedral : 18.199 80.528 910 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.97 % Allowed : 15.75 % Favored : 83.28 % Rotamer: Outliers : 17.11 % Allowed : 23.53 % Favored : 59.36 % 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: -3.42 (0.32), residues: 616 helix: -0.96 (0.24), residues: 376 sheet: -5.13 (1.10), residues: 10 loop : -4.44 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 10 HIS 0.009 0.001 HIS A 247 PHE 0.018 0.002 PHE A 68 TYR 0.016 0.002 TYR A 139 ARG 0.006 0.001 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 155 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.6123 (OUTLIER) cc_final: 0.5456 (mp) REVERT: A 429 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6938 (mm) REVERT: A 442 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.8054 (pt) REVERT: A 570 MET cc_start: 0.6998 (mmm) cc_final: 0.6765 (mmt) outliers start: 96 outliers final: 54 residues processed: 217 average time/residue: 0.1683 time to fit residues: 46.7813 Evaluate side-chains 185 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 128 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 531 TRP Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 711 CYS Chi-restraints excluded: chain A residue 712 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 46 optimal weight: 0.1980 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 GLN ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5283 Z= 0.273 Angle : 0.777 9.733 7163 Z= 0.392 Chirality : 0.044 0.160 815 Planarity : 0.007 0.077 869 Dihedral : 14.840 79.836 798 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.65 % Allowed : 14.94 % Favored : 84.42 % Rotamer: Outliers : 11.41 % Allowed : 28.16 % Favored : 60.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.33), residues: 616 helix: -0.29 (0.26), residues: 368 sheet: -4.93 (1.16), residues: 10 loop : -4.13 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 76 HIS 0.005 0.001 HIS A 247 PHE 0.014 0.001 PHE A 565 TYR 0.030 0.002 TYR A 264 ARG 0.013 0.001 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 127 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7419 (mm) REVERT: A 442 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7957 (pt) REVERT: A 650 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7873 (mp) outliers start: 64 outliers final: 42 residues processed: 172 average time/residue: 0.1554 time to fit residues: 34.6495 Evaluate side-chains 157 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 112 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 531 TRP Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 616 CYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 711 CYS Chi-restraints excluded: chain A residue 712 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 53 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.5730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5283 Z= 0.229 Angle : 0.721 9.155 7163 Z= 0.364 Chirality : 0.042 0.141 815 Planarity : 0.006 0.069 869 Dihedral : 13.565 76.885 778 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.49 % Allowed : 12.82 % Favored : 86.69 % Rotamer: Outliers : 10.34 % Allowed : 29.41 % Favored : 60.25 % 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: -2.24 (0.34), residues: 616 helix: -0.02 (0.26), residues: 373 sheet: -3.96 (1.24), residues: 15 loop : -3.92 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 76 HIS 0.008 0.001 HIS A 247 PHE 0.013 0.001 PHE A 565 TYR 0.035 0.002 TYR A 78 ARG 0.009 0.001 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 124 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 TYR cc_start: 0.5352 (p90) cc_final: 0.4666 (p90) REVERT: A 503 MET cc_start: 0.7180 (tmm) cc_final: 0.6847 (ttp) REVERT: A 650 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7872 (mp) outliers start: 58 outliers final: 41 residues processed: 164 average time/residue: 0.1571 time to fit residues: 33.6753 Evaluate side-chains 153 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 111 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 531 TRP Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 711 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.6135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5283 Z= 0.282 Angle : 0.743 8.921 7163 Z= 0.371 Chirality : 0.044 0.143 815 Planarity : 0.007 0.067 869 Dihedral : 13.095 73.833 768 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.49 % Allowed : 13.31 % Favored : 86.20 % Rotamer: Outliers : 10.34 % Allowed : 28.34 % Favored : 61.32 % 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: -1.82 (0.34), residues: 616 helix: 0.32 (0.27), residues: 361 sheet: -3.74 (1.32), residues: 15 loop : -3.58 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 473 HIS 0.006 0.001 HIS A 247 PHE 0.015 0.001 PHE A 565 TYR 0.044 0.002 TYR A 78 ARG 0.006 0.001 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 118 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.5942 (OUTLIER) cc_final: 0.5241 (mp) REVERT: A 75 PHE cc_start: 0.7319 (OUTLIER) cc_final: 0.6946 (t80) REVERT: A 199 PHE cc_start: 0.7167 (OUTLIER) cc_final: 0.6918 (t80) REVERT: A 237 ARG cc_start: 0.6745 (OUTLIER) cc_final: 0.6247 (ttm-80) REVERT: A 406 ILE cc_start: 0.8395 (tt) cc_final: 0.7942 (tt) REVERT: A 499 ASN cc_start: 0.6459 (t0) cc_final: 0.6217 (t0) REVERT: A 503 MET cc_start: 0.7393 (tmm) cc_final: 0.6893 (ttp) outliers start: 58 outliers final: 42 residues processed: 156 average time/residue: 0.1738 time to fit residues: 34.8743 Evaluate side-chains 154 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 108 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 430 PHE Chi-restraints excluded: chain A residue 435 PHE Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 531 TRP Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 595 ARG Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 711 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 0.0060 chunk 57 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.6328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5283 Z= 0.223 Angle : 0.690 9.334 7163 Z= 0.341 Chirality : 0.041 0.135 815 Planarity : 0.006 0.068 869 Dihedral : 12.101 63.357 765 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.49 % Allowed : 12.50 % Favored : 87.01 % Rotamer: Outliers : 9.98 % Allowed : 29.59 % Favored : 60.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.35), residues: 616 helix: 0.60 (0.27), residues: 362 sheet: -3.66 (1.40), residues: 15 loop : -3.52 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 473 HIS 0.006 0.001 HIS A 247 PHE 0.014 0.001 PHE A 565 TYR 0.039 0.002 TYR A 78 ARG 0.004 0.001 ARG A 574 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 117 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.5813 (OUTLIER) cc_final: 0.5106 (mp) REVERT: A 75 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.6897 (t80) REVERT: A 199 PHE cc_start: 0.7175 (OUTLIER) cc_final: 0.6943 (t80) REVERT: A 237 ARG cc_start: 0.6700 (OUTLIER) cc_final: 0.6158 (ttm-80) REVERT: A 398 THR cc_start: 0.8343 (p) cc_final: 0.8142 (p) REVERT: A 406 ILE cc_start: 0.8418 (tt) cc_final: 0.7985 (tt) REVERT: A 499 ASN cc_start: 0.6389 (t0) cc_final: 0.6055 (t0) REVERT: A 503 MET cc_start: 0.7353 (tmm) cc_final: 0.6844 (ttp) REVERT: A 672 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7364 (mm) outliers start: 56 outliers final: 35 residues processed: 155 average time/residue: 0.1722 time to fit residues: 34.7488 Evaluate side-chains 152 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 112 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 531 TRP Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 711 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 0.0270 chunk 35 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.6512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5283 Z= 0.210 Angle : 0.695 8.876 7163 Z= 0.338 Chirality : 0.042 0.238 815 Planarity : 0.006 0.066 869 Dihedral : 10.978 56.448 755 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.18 % Favored : 87.50 % Rotamer: Outliers : 9.98 % Allowed : 29.23 % Favored : 60.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.36), residues: 616 helix: 0.81 (0.27), residues: 360 sheet: -3.55 (1.44), residues: 15 loop : -3.34 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 473 HIS 0.005 0.001 HIS A 247 PHE 0.016 0.001 PHE A 699 TYR 0.031 0.002 TYR A 78 ARG 0.008 0.001 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 113 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.5796 (OUTLIER) cc_final: 0.5105 (mp) REVERT: A 199 PHE cc_start: 0.7182 (OUTLIER) cc_final: 0.6972 (t80) REVERT: A 237 ARG cc_start: 0.6676 (OUTLIER) cc_final: 0.6136 (ttm-80) REVERT: A 406 ILE cc_start: 0.8449 (tt) cc_final: 0.7985 (tt) REVERT: A 423 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7087 (tt) REVERT: A 499 ASN cc_start: 0.6330 (t0) cc_final: 0.6029 (t0) REVERT: A 503 MET cc_start: 0.7349 (tmm) cc_final: 0.6917 (ttp) REVERT: A 672 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7345 (mm) outliers start: 56 outliers final: 41 residues processed: 148 average time/residue: 0.1660 time to fit residues: 31.8643 Evaluate side-chains 159 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 113 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 430 PHE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 PHE Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 531 TRP Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 711 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 7.9990 chunk 5 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 54 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 190 ASN ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 GLN ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.6619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5283 Z= 0.212 Angle : 0.680 7.982 7163 Z= 0.337 Chirality : 0.041 0.166 815 Planarity : 0.006 0.065 869 Dihedral : 10.524 55.725 755 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.34 % Favored : 87.34 % Rotamer: Outliers : 9.98 % Allowed : 28.88 % Favored : 61.14 % 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: -1.08 (0.36), residues: 616 helix: 0.89 (0.28), residues: 360 sheet: -3.55 (1.46), residues: 15 loop : -3.19 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 473 HIS 0.004 0.001 HIS A 247 PHE 0.016 0.001 PHE A 699 TYR 0.031 0.002 TYR A 264 ARG 0.010 0.001 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 119 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6932 (mm) REVERT: A 237 ARG cc_start: 0.6700 (OUTLIER) cc_final: 0.6115 (ttm-80) REVERT: A 406 ILE cc_start: 0.8428 (tt) cc_final: 0.7972 (tt) REVERT: A 423 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7024 (tt) REVERT: A 499 ASN cc_start: 0.6362 (t0) cc_final: 0.6037 (t0) REVERT: A 503 MET cc_start: 0.7376 (tmm) cc_final: 0.7053 (ttp) REVERT: A 531 TRP cc_start: 0.7557 (OUTLIER) cc_final: 0.7212 (t60) outliers start: 56 outliers final: 39 residues processed: 157 average time/residue: 0.1616 time to fit residues: 33.0896 Evaluate side-chains 154 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 111 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 430 PHE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 PHE Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 531 TRP Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 711 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.4980 chunk 43 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.6721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5283 Z= 0.232 Angle : 0.687 7.524 7163 Z= 0.342 Chirality : 0.042 0.166 815 Planarity : 0.006 0.064 869 Dihedral : 10.277 60.416 751 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.01 % Favored : 87.66 % Rotamer: Outliers : 8.91 % Allowed : 30.12 % Favored : 60.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.36), residues: 616 helix: 0.92 (0.27), residues: 361 sheet: -3.58 (1.43), residues: 15 loop : -3.22 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 422 HIS 0.003 0.001 HIS A 247 PHE 0.018 0.001 PHE A 699 TYR 0.030 0.002 TYR A 264 ARG 0.009 0.000 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 117 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.5922 (OUTLIER) cc_final: 0.5209 (mp) REVERT: A 237 ARG cc_start: 0.6715 (OUTLIER) cc_final: 0.6062 (ttm-80) REVERT: A 406 ILE cc_start: 0.8441 (tt) cc_final: 0.7999 (tt) REVERT: A 423 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7033 (tt) REVERT: A 499 ASN cc_start: 0.6344 (t0) cc_final: 0.6012 (t0) REVERT: A 503 MET cc_start: 0.7269 (tmm) cc_final: 0.6933 (ttp) REVERT: A 531 TRP cc_start: 0.7579 (OUTLIER) cc_final: 0.7229 (t60) outliers start: 50 outliers final: 37 residues processed: 148 average time/residue: 0.1618 time to fit residues: 31.4030 Evaluate side-chains 154 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 113 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 PHE Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 531 TRP Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 711 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.9980 chunk 56 optimal weight: 0.0980 chunk 49 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 7 optimal weight: 0.0770 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.6912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5283 Z= 0.202 Angle : 0.695 8.318 7163 Z= 0.344 Chirality : 0.042 0.225 815 Planarity : 0.006 0.067 869 Dihedral : 9.843 64.167 747 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.69 % Favored : 87.99 % Rotamer: Outliers : 7.84 % Allowed : 31.19 % Favored : 60.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.36), residues: 616 helix: 0.86 (0.27), residues: 372 sheet: -3.62 (1.38), residues: 15 loop : -3.32 (0.43), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 422 HIS 0.003 0.001 HIS A 247 PHE 0.019 0.001 PHE A 699 TYR 0.028 0.002 TYR A 264 ARG 0.011 0.001 ARG A 340 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 119 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.6991 (t80) REVERT: A 237 ARG cc_start: 0.6658 (OUTLIER) cc_final: 0.6083 (ttm-80) REVERT: A 406 ILE cc_start: 0.8467 (tt) cc_final: 0.8035 (tt) REVERT: A 423 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7025 (tt) REVERT: A 499 ASN cc_start: 0.6244 (t0) cc_final: 0.5920 (t0) REVERT: A 503 MET cc_start: 0.7177 (tmm) cc_final: 0.6955 (ttp) REVERT: A 531 TRP cc_start: 0.7519 (OUTLIER) cc_final: 0.7191 (t60) outliers start: 44 outliers final: 29 residues processed: 145 average time/residue: 0.1700 time to fit residues: 32.2263 Evaluate side-chains 150 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 117 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 531 TRP Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 711 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 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 187 GLN ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 HIS ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.171706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.128192 restraints weight = 7152.298| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.91 r_work: 0.3565 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.6904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5283 Z= 0.250 Angle : 0.704 10.737 7163 Z= 0.352 Chirality : 0.043 0.211 815 Planarity : 0.006 0.063 869 Dihedral : 9.562 70.271 742 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.85 % Favored : 87.82 % Rotamer: Outliers : 6.42 % Allowed : 32.26 % Favored : 61.32 % 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: -1.15 (0.36), residues: 616 helix: 0.77 (0.27), residues: 376 sheet: -3.65 (1.38), residues: 15 loop : -3.35 (0.44), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 422 HIS 0.003 0.001 HIS A 247 PHE 0.014 0.001 PHE A 701 TYR 0.026 0.002 TYR A 264 ARG 0.012 0.001 ARG A 340 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1762.41 seconds wall clock time: 32 minutes 20.10 seconds (1940.10 seconds total)