Starting phenix.real_space_refine on Sun Mar 10 22:35:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmf_27535/03_2024/8dmf_27535_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmf_27535/03_2024/8dmf_27535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmf_27535/03_2024/8dmf_27535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmf_27535/03_2024/8dmf_27535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmf_27535/03_2024/8dmf_27535_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmf_27535/03_2024/8dmf_27535_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 33 5.16 5 C 3589 2.51 5 N 951 2.21 5 O 1093 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 697": "OE1" <-> "OE2" 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: 5670 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5670 Unusual residues: {' MG': 1, 'GTP': 1} Inner-chain residues flagged as termini: ['pdbres="GLU A 718 "'] Classifications: {'peptide': 718, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 685, None: 2} Not linked: pdbres="GLU A 718 " pdbres=" MG A 801 " Not linked: pdbres=" MG A 801 " pdbres="GTP A 802 " Time building chain proxies: 3.73, per 1000 atoms: 0.66 Number of scatterers: 5670 At special positions: 0 Unit cell: (75.828, 72.624, 127.092, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 33 16.00 P 3 15.00 Mg 1 11.99 O 1093 8.00 N 951 7.00 C 3589 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: 2.20 Conformation dependent library (CDL) restraints added in 1.2 seconds 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1312 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 9 sheets defined 28.1% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 6 through 8 No H-bonds generated for 'chain 'A' and resid 6 through 8' Processing helix chain 'A' and resid 22 through 33 Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'A' and resid 88 through 97 Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 143 through 153 Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 199 through 219 removed outlier: 4.749A pdb=" N ASP A 203 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 204 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET A 208 " --> pdb=" O ALA A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 247 removed outlier: 4.231A pdb=" N GLU A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 274 Processing helix chain 'A' and resid 412 through 425 Processing helix chain 'A' and resid 447 through 458 Processing helix chain 'A' and resid 556 through 570 Proline residue: A 560 - end of helix Processing helix chain 'A' and resid 599 through 616 Processing helix chain 'A' and resid 634 through 647 removed outlier: 5.340A pdb=" N GLY A 638 " --> pdb=" O ASP A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 671 No H-bonds generated for 'chain 'A' and resid 669 through 671' Processing helix chain 'A' and resid 675 through 683 Processing helix chain 'A' and resid 701 through 717 removed outlier: 4.207A pdb=" N GLU A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 254 through 256 removed outlier: 9.341A pdb=" N PHE A 255 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N PHE A 131 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS A 75 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE A 12 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ASN A 77 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU A 14 " --> pdb=" O ASN A 77 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE A 79 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 162 through 164 Processing sheet with id= C, first strand: chain 'A' and resid 380 through 382 removed outlier: 3.671A pdb=" N SER A 302 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 324 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TYR A 304 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL A 322 " --> pdb=" O TYR A 304 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 347 through 350 removed outlier: 4.477A pdb=" N ILE A 347 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 465 through 468 removed outlier: 3.912A pdb=" N TYR A 400 " --> pdb=" O GLY A 444 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR A 440 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A 439 " --> pdb=" O SER A 434 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 475 through 478 Processing sheet with id= G, first strand: chain 'A' and resid 482 through 488 removed outlier: 3.539A pdb=" N ALA A 482 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP A 589 " --> pdb=" O HIS A 502 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A 504 " --> pdb=" O VAL A 587 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N VAL A 587 " --> pdb=" O ILE A 504 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLU A 506 " --> pdb=" O VAL A 585 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N VAL A 585 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 534 through 536 Processing sheet with id= I, first strand: chain 'A' and resid 691 through 693 removed outlier: 3.545A pdb=" N GLY A 653 " --> pdb=" O VAL A 664 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LYS A 666 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ILE A 651 " --> pdb=" O LYS A 666 " (cutoff:3.500A) 197 hydrogen bonds defined for protein. 468 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: 1.69 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1743 1.33 - 1.45: 846 1.45 - 1.57: 3124 1.57 - 1.69: 5 1.69 - 1.81: 61 Bond restraints: 5779 Sorted by residual: bond pdb=" N GLU A 476 " pdb=" CA GLU A 476 " ideal model delta sigma weight residual 1.452 1.488 -0.035 1.25e-02 6.40e+03 7.96e+00 bond pdb=" N GLU A 697 " pdb=" CA GLU A 697 " ideal model delta sigma weight residual 1.455 1.489 -0.033 1.32e-02 5.74e+03 6.38e+00 bond pdb=" N TYR A 474 " pdb=" CA TYR A 474 " ideal model delta sigma weight residual 1.455 1.486 -0.030 1.22e-02 6.72e+03 6.21e+00 bond pdb=" N LYS A 22 " pdb=" CA LYS A 22 " ideal model delta sigma weight residual 1.460 1.490 -0.030 1.22e-02 6.72e+03 6.10e+00 bond pdb=" N SER A 695 " pdb=" CA SER A 695 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.21e-02 6.83e+03 5.63e+00 ... (remaining 5774 not shown) Histogram of bond angle deviations from ideal: 98.82 - 105.87: 148 105.87 - 112.92: 3041 112.92 - 119.98: 2007 119.98 - 127.03: 2549 127.03 - 134.08: 50 Bond angle restraints: 7795 Sorted by residual: angle pdb=" N GLU A 425 " pdb=" CA GLU A 425 " pdb=" C GLU A 425 " ideal model delta sigma weight residual 111.28 107.47 3.81 1.09e+00 8.42e-01 1.22e+01 angle pdb=" CA GLU A 697 " pdb=" C GLU A 697 " pdb=" O GLU A 697 " ideal model delta sigma weight residual 121.36 118.00 3.36 1.06e+00 8.90e-01 1.00e+01 angle pdb=" N GLU A 424 " pdb=" CA GLU A 424 " pdb=" C GLU A 424 " ideal model delta sigma weight residual 111.71 108.17 3.54 1.15e+00 7.56e-01 9.47e+00 angle pdb=" CA GLU A 476 " pdb=" C GLU A 476 " pdb=" O GLU A 476 " ideal model delta sigma weight residual 121.82 118.12 3.70 1.21e+00 6.83e-01 9.36e+00 angle pdb=" CA TYR A 696 " pdb=" C TYR A 696 " pdb=" O TYR A 696 " ideal model delta sigma weight residual 121.55 118.32 3.23 1.06e+00 8.90e-01 9.28e+00 ... (remaining 7790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.34: 3265 22.34 - 44.68: 233 44.68 - 67.02: 10 67.02 - 89.36: 3 89.36 - 111.70: 4 Dihedral angle restraints: 3515 sinusoidal: 1461 harmonic: 2054 Sorted by residual: dihedral pdb=" C8 GTP A 802 " pdb=" C1' GTP A 802 " pdb=" N9 GTP A 802 " pdb=" O4' GTP A 802 " ideal model delta sinusoidal sigma weight residual 104.59 -7.11 111.70 1 2.00e+01 2.50e-03 3.29e+01 dihedral pdb=" C5' GTP A 802 " pdb=" O5' GTP A 802 " pdb=" PA GTP A 802 " pdb=" O3A GTP A 802 " ideal model delta sinusoidal sigma weight residual 69.27 178.40 -109.13 1 2.00e+01 2.50e-03 3.19e+01 dihedral pdb=" CA MET A 224 " pdb=" C MET A 224 " pdb=" N GLU A 225 " pdb=" CA GLU A 225 " ideal model delta harmonic sigma weight residual -180.00 -159.71 -20.29 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 3512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 573 0.037 - 0.073: 172 0.073 - 0.110: 76 0.110 - 0.146: 22 0.146 - 0.183: 3 Chirality restraints: 846 Sorted by residual: chirality pdb=" CB ILE A 535 " pdb=" CA ILE A 535 " pdb=" CG1 ILE A 535 " pdb=" CG2 ILE A 535 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" CA GLU A 424 " pdb=" N GLU A 424 " pdb=" C GLU A 424 " pdb=" CB GLU A 424 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" CA ARG A 423 " pdb=" N ARG A 423 " pdb=" C ARG A 423 " pdb=" CB ARG A 423 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.15 2.00e-01 2.50e+01 5.98e-01 ... (remaining 843 not shown) Planarity restraints: 1012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 632 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO A 633 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 633 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 633 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 276 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO A 277 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 277 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 277 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 21 " -0.005 2.00e-02 2.50e+03 1.05e-02 1.10e+00 pdb=" C GLY A 21 " 0.018 2.00e-02 2.50e+03 pdb=" O GLY A 21 " -0.007 2.00e-02 2.50e+03 pdb=" N LYS A 22 " -0.006 2.00e-02 2.50e+03 ... (remaining 1009 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 66 2.56 - 3.15: 4822 3.15 - 3.73: 9310 3.73 - 4.32: 11970 4.32 - 4.90: 19666 Nonbonded interactions: 45834 Sorted by model distance: nonbonded pdb="MG MG A 801 " pdb=" O3A GTP A 802 " model vdw 1.977 2.170 nonbonded pdb="MG MG A 801 " pdb=" O3G GTP A 802 " model vdw 2.168 2.170 nonbonded pdb=" N THR A 23 " pdb="MG MG A 801 " model vdw 2.183 2.250 nonbonded pdb=" OH TYR A 400 " pdb=" NH2 ARG A 402 " model vdw 2.257 2.520 nonbonded pdb=" NZ LYS A 291 " pdb=" OH TYR A 388 " model vdw 2.267 2.520 ... (remaining 45829 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.170 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: 1.110 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.250 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5779 Z= 0.185 Angle : 0.636 8.154 7795 Z= 0.347 Chirality : 0.046 0.183 846 Planarity : 0.004 0.042 1012 Dihedral : 14.277 111.705 2203 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: -0.20 (0.33), residues: 716 helix: 1.11 (0.39), residues: 202 sheet: -0.03 (0.41), residues: 195 loop : -0.97 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 455 HIS 0.009 0.001 HIS A 449 PHE 0.011 0.001 PHE A 610 TYR 0.008 0.001 TYR A 696 ARG 0.002 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 208 MET cc_start: 0.8795 (ptm) cc_final: 0.8594 (ttt) REVERT: A 251 MET cc_start: 0.8929 (tmm) cc_final: 0.8647 (tmm) REVERT: A 263 MET cc_start: 0.8783 (mmp) cc_final: 0.8097 (mmp) REVERT: A 323 MET cc_start: 0.8461 (mmp) cc_final: 0.8205 (mmm) REVERT: A 563 MET cc_start: 0.9575 (mmp) cc_final: 0.9122 (mmm) REVERT: A 650 MET cc_start: 0.9167 (mpp) cc_final: 0.8874 (mpp) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1508 time to fit residues: 10.0720 Evaluate side-chains 36 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 30.0000 chunk 29 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 65 optimal weight: 0.5980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 443 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 5779 Z= 0.152 Angle : 0.578 9.789 7795 Z= 0.289 Chirality : 0.044 0.151 846 Planarity : 0.004 0.032 1012 Dihedral : 7.348 109.875 787 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.33 % Allowed : 8.97 % Favored : 90.70 % 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 (0.33), residues: 716 helix: 0.92 (0.38), residues: 201 sheet: 0.17 (0.41), residues: 198 loop : -0.93 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 429 HIS 0.007 0.001 HIS A 449 PHE 0.007 0.001 PHE A 255 TYR 0.009 0.001 TYR A 121 ARG 0.003 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.730 Fit side-chains REVERT: A 251 MET cc_start: 0.8944 (tmm) cc_final: 0.8671 (tmm) REVERT: A 263 MET cc_start: 0.8685 (mmp) cc_final: 0.7886 (mmp) REVERT: A 323 MET cc_start: 0.8504 (mmp) cc_final: 0.8190 (mmm) REVERT: A 394 LYS cc_start: 0.9193 (tppt) cc_final: 0.8925 (tptp) REVERT: A 563 MET cc_start: 0.9514 (mmp) cc_final: 0.9164 (mmm) REVERT: A 567 MET cc_start: 0.9356 (mpp) cc_final: 0.9071 (mpp) outliers start: 2 outliers final: 1 residues processed: 44 average time/residue: 0.1590 time to fit residues: 10.0616 Evaluate side-chains 38 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 30.0000 chunk 44 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 overall best weight: 5.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5779 Z= 0.225 Angle : 0.584 8.434 7795 Z= 0.295 Chirality : 0.043 0.170 846 Planarity : 0.004 0.031 1012 Dihedral : 7.573 112.497 787 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.98 % Allowed : 12.40 % Favored : 86.62 % 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: -0.31 (0.32), residues: 716 helix: 0.65 (0.37), residues: 200 sheet: 0.20 (0.41), residues: 198 loop : -0.97 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 429 HIS 0.005 0.001 HIS A 449 PHE 0.008 0.001 PHE A 525 TYR 0.014 0.001 TYR A 121 ARG 0.003 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.9204 (mmt) cc_final: 0.8683 (mpp) REVERT: A 251 MET cc_start: 0.8979 (tmm) cc_final: 0.8765 (tmm) REVERT: A 323 MET cc_start: 0.8574 (mmp) cc_final: 0.8241 (mmm) REVERT: A 394 LYS cc_start: 0.9266 (tppt) cc_final: 0.9041 (tptp) REVERT: A 563 MET cc_start: 0.9439 (mmp) cc_final: 0.9071 (mmm) REVERT: A 567 MET cc_start: 0.9433 (mpp) cc_final: 0.9170 (mpp) outliers start: 6 outliers final: 3 residues processed: 43 average time/residue: 0.1655 time to fit residues: 10.2537 Evaluate side-chains 39 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 712 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 33 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 0.3980 chunk 69 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5779 Z= 0.203 Angle : 0.574 8.389 7795 Z= 0.286 Chirality : 0.042 0.138 846 Planarity : 0.004 0.030 1012 Dihedral : 7.507 111.652 787 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.98 % Allowed : 15.17 % Favored : 83.85 % 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: -0.27 (0.32), residues: 716 helix: 0.70 (0.38), residues: 202 sheet: 0.15 (0.41), residues: 198 loop : -0.91 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 429 HIS 0.006 0.001 HIS A 449 PHE 0.013 0.001 PHE A 255 TYR 0.012 0.001 TYR A 121 ARG 0.005 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.9164 (mmt) cc_final: 0.8687 (mpp) REVERT: A 251 MET cc_start: 0.9000 (tmm) cc_final: 0.8780 (tmm) REVERT: A 323 MET cc_start: 0.8551 (mmp) cc_final: 0.8143 (mmm) REVERT: A 563 MET cc_start: 0.9441 (mmp) cc_final: 0.9098 (mmm) outliers start: 6 outliers final: 6 residues processed: 42 average time/residue: 0.1624 time to fit residues: 9.7463 Evaluate side-chains 43 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 712 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 28 optimal weight: 20.0000 chunk 59 optimal weight: 8.9990 chunk 48 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 5779 Z= 0.255 Angle : 0.603 7.729 7795 Z= 0.305 Chirality : 0.043 0.137 846 Planarity : 0.004 0.032 1012 Dihedral : 7.636 112.590 787 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.96 % Allowed : 15.33 % Favored : 82.71 % 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: -0.47 (0.32), residues: 716 helix: 0.44 (0.36), residues: 204 sheet: 0.07 (0.41), residues: 196 loop : -0.99 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 429 HIS 0.005 0.002 HIS A 449 PHE 0.011 0.001 PHE A 255 TYR 0.014 0.001 TYR A 121 ARG 0.005 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 37 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.9177 (mmp) cc_final: 0.8965 (mmm) REVERT: A 251 MET cc_start: 0.9055 (tmm) cc_final: 0.8827 (tmm) REVERT: A 323 MET cc_start: 0.8531 (mmp) cc_final: 0.8136 (mmm) REVERT: A 424 GLU cc_start: 0.9354 (mm-30) cc_final: 0.8821 (mm-30) REVERT: A 563 MET cc_start: 0.9420 (mmp) cc_final: 0.9191 (mmm) outliers start: 12 outliers final: 7 residues processed: 46 average time/residue: 0.1532 time to fit residues: 10.1479 Evaluate side-chains 42 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 571 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 17 optimal weight: 30.0000 chunk 69 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 overall best weight: 6.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5779 Z= 0.276 Angle : 0.623 8.364 7795 Z= 0.313 Chirality : 0.043 0.154 846 Planarity : 0.004 0.029 1012 Dihedral : 7.663 112.075 787 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.31 % Allowed : 17.46 % Favored : 81.24 % 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: -0.57 (0.32), residues: 716 helix: 0.35 (0.36), residues: 204 sheet: 0.03 (0.41), residues: 196 loop : -1.05 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 429 HIS 0.011 0.002 HIS A 449 PHE 0.011 0.001 PHE A 610 TYR 0.015 0.001 TYR A 121 ARG 0.005 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 36 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.9037 (tmm) cc_final: 0.8786 (tmm) REVERT: A 323 MET cc_start: 0.8587 (mmp) cc_final: 0.8178 (mmm) REVERT: A 424 GLU cc_start: 0.9366 (mm-30) cc_final: 0.8959 (mm-30) outliers start: 8 outliers final: 6 residues processed: 42 average time/residue: 0.1490 time to fit residues: 9.3080 Evaluate side-chains 42 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 712 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 42 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 5779 Z= 0.263 Angle : 0.619 7.958 7795 Z= 0.310 Chirality : 0.043 0.153 846 Planarity : 0.004 0.030 1012 Dihedral : 7.570 111.241 787 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.79 % Allowed : 18.27 % Favored : 79.93 % 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: -0.61 (0.32), residues: 716 helix: 0.28 (0.37), residues: 199 sheet: 0.13 (0.42), residues: 189 loop : -1.11 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 429 HIS 0.012 0.002 HIS A 449 PHE 0.012 0.001 PHE A 545 TYR 0.014 0.001 TYR A 121 ARG 0.005 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 202 MET cc_start: 0.9065 (tpp) cc_final: 0.8859 (tpp) REVERT: A 251 MET cc_start: 0.9010 (tmm) cc_final: 0.8781 (tmm) REVERT: A 323 MET cc_start: 0.8602 (mmp) cc_final: 0.8184 (mmm) REVERT: A 424 GLU cc_start: 0.9377 (mm-30) cc_final: 0.8956 (mm-30) outliers start: 11 outliers final: 6 residues processed: 47 average time/residue: 0.1401 time to fit residues: 9.7312 Evaluate side-chains 43 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 447 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 chunk 60 optimal weight: 30.0000 chunk 64 optimal weight: 6.9990 overall best weight: 7.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 5779 Z= 0.303 Angle : 0.669 9.826 7795 Z= 0.333 Chirality : 0.044 0.151 846 Planarity : 0.004 0.031 1012 Dihedral : 7.632 112.175 787 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 21.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 1.63 % Allowed : 20.39 % Favored : 77.98 % 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: -0.75 (0.32), residues: 716 helix: 0.09 (0.36), residues: 200 sheet: -0.01 (0.42), residues: 191 loop : -1.11 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 429 HIS 0.011 0.002 HIS A 449 PHE 0.014 0.001 PHE A 525 TYR 0.015 0.001 TYR A 121 ARG 0.003 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 36 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: A 95 LEU cc_start: 0.9658 (OUTLIER) cc_final: 0.9391 (mm) REVERT: A 251 MET cc_start: 0.9016 (tmm) cc_final: 0.8784 (tmm) REVERT: A 323 MET cc_start: 0.8624 (mmp) cc_final: 0.8186 (mmm) REVERT: A 424 GLU cc_start: 0.9374 (mm-30) cc_final: 0.8937 (mm-30) outliers start: 10 outliers final: 7 residues processed: 43 average time/residue: 0.1442 time to fit residues: 9.2341 Evaluate side-chains 44 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 36 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 337 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 28 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5779 Z= 0.227 Angle : 0.640 9.232 7795 Z= 0.314 Chirality : 0.044 0.141 846 Planarity : 0.004 0.030 1012 Dihedral : 7.353 110.012 787 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.31 % Allowed : 20.88 % Favored : 77.81 % 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: -0.63 (0.32), residues: 716 helix: 0.31 (0.37), residues: 194 sheet: 0.01 (0.42), residues: 193 loop : -1.08 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 429 HIS 0.010 0.002 HIS A 449 PHE 0.009 0.001 PHE A 255 TYR 0.012 0.001 TYR A 121 ARG 0.004 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 95 LEU cc_start: 0.9651 (OUTLIER) cc_final: 0.9396 (mm) REVERT: A 323 MET cc_start: 0.8608 (mmp) cc_final: 0.8176 (mmm) REVERT: A 424 GLU cc_start: 0.9349 (mm-30) cc_final: 0.8905 (mm-30) outliers start: 8 outliers final: 5 residues processed: 44 average time/residue: 0.1495 time to fit residues: 9.7816 Evaluate side-chains 44 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 337 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 5 optimal weight: 0.0040 chunk 44 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 60 optimal weight: 20.0000 chunk 17 optimal weight: 0.3980 overall best weight: 4.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN A 488 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5779 Z= 0.199 Angle : 0.656 9.326 7795 Z= 0.318 Chirality : 0.044 0.171 846 Planarity : 0.004 0.031 1012 Dihedral : 7.154 108.765 787 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.82 % Allowed : 21.70 % Favored : 77.49 % 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: -0.60 (0.32), residues: 716 helix: 0.19 (0.37), residues: 200 sheet: 0.09 (0.43), residues: 191 loop : -1.00 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 429 HIS 0.011 0.002 HIS A 449 PHE 0.008 0.001 PHE A 255 TYR 0.011 0.001 TYR A 121 ARG 0.003 0.000 ARG A 239 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: A 95 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9388 (mm) REVERT: A 323 MET cc_start: 0.8617 (mmp) cc_final: 0.8186 (mmm) REVERT: A 424 GLU cc_start: 0.9343 (mm-30) cc_final: 0.8889 (mm-30) REVERT: A 660 PHE cc_start: 0.9419 (m-80) cc_final: 0.9161 (m-10) outliers start: 5 outliers final: 4 residues processed: 43 average time/residue: 0.1481 time to fit residues: 9.4360 Evaluate side-chains 44 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 337 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 23 optimal weight: 30.0000 chunk 58 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 50 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.038450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.030613 restraints weight = 49528.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.031570 restraints weight = 29944.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.032264 restraints weight = 20996.437| |-----------------------------------------------------------------------------| r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5779 Z= 0.295 Angle : 0.696 8.785 7795 Z= 0.344 Chirality : 0.044 0.152 846 Planarity : 0.004 0.031 1012 Dihedral : 7.416 112.002 787 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 21.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 1.31 % Allowed : 21.70 % Favored : 77.00 % 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: -0.69 (0.32), residues: 716 helix: 0.15 (0.37), residues: 194 sheet: 0.16 (0.43), residues: 185 loop : -1.14 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 429 HIS 0.010 0.002 HIS A 449 PHE 0.014 0.001 PHE A 525 TYR 0.014 0.001 TYR A 121 ARG 0.004 0.000 ARG A 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1138.99 seconds wall clock time: 21 minutes 44.34 seconds (1304.34 seconds total)