Starting phenix.real_space_refine on Fri Apr 5 15:22:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhq_36284/04_2024/8jhq_36284_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhq_36284/04_2024/8jhq_36284.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhq_36284/04_2024/8jhq_36284_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhq_36284/04_2024/8jhq_36284_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhq_36284/04_2024/8jhq_36284_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhq_36284/04_2024/8jhq_36284.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhq_36284/04_2024/8jhq_36284.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhq_36284/04_2024/8jhq_36284_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhq_36284/04_2024/8jhq_36284_updated.pdb" } resolution = 3.6 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= 0.030 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 19 5.16 5 C 2235 2.51 5 N 571 2.21 5 O 594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A ASP 220": "OD1" <-> "OD2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 558": "OD1" <-> "OD2" Residue "A GLU 629": "OE1" <-> "OE2" Residue "A PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 721": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 3420 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3395 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 14, 'TRANS': 431} Chain breaks: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'S1P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.34, per 1000 atoms: 0.68 Number of scatterers: 3420 At special positions: 0 Unit cell: (88.4, 62.9, 66.3, 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 19 16.00 P 1 15.00 O 594 8.00 N 571 7.00 C 2235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 549 " - pdb=" SG CYS A 554 " distance=2.03 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: 1.46 Conformation dependent library (CDL) restraints added in 652.6 milliseconds 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 808 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 0 sheets defined 79.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 100 through 120 removed outlier: 3.892A pdb=" N ALA A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 137 through 164 removed outlier: 3.828A pdb=" N LEU A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLN A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Proline residue: A 156 - end of helix removed outlier: 3.725A pdb=" N ARG A 164 " --> pdb=" O TYR A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 187 removed outlier: 3.881A pdb=" N SER A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N PHE A 187 " --> pdb=" O PHE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 211 removed outlier: 3.605A pdb=" N ALA A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 removed outlier: 3.778A pdb=" N ILE A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 452 removed outlier: 4.377A pdb=" N ILE A 434 " --> pdb=" O PHE A 430 " (cutoff:3.500A) Proline residue: A 435 - end of helix Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 462 through 475 removed outlier: 3.948A pdb=" N GLY A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR A 471 " --> pdb=" O MET A 467 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 472 " --> pdb=" O ILE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.576A pdb=" N ALA A 504 " --> pdb=" O ARG A 500 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG A 507 " --> pdb=" O LYS A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 542 Proline residue: A 533 - end of helix Processing helix chain 'A' and resid 557 through 586 removed outlier: 4.231A pdb=" N PHE A 571 " --> pdb=" O CYS A 567 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 613 removed outlier: 3.894A pdb=" N PHE A 611 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL A 612 " --> pdb=" O CYS A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 646 removed outlier: 4.845A pdb=" N ASN A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N TRP A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ALA A 637 " --> pdb=" O PHE A 633 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ILE A 638 " --> pdb=" O SER A 634 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A 640 " --> pdb=" O TRP A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 665 removed outlier: 3.935A pdb=" N SER A 660 " --> pdb=" O VAL A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 684 Processing helix chain 'A' and resid 690 through 736 removed outlier: 4.356A pdb=" N LEU A 703 " --> pdb=" O TYR A 699 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N CYS A 704 " --> pdb=" O ALA A 700 " (cutoff:3.500A) Proline residue: A 705 - end of helix removed outlier: 3.584A pdb=" N PHE A 721 " --> pdb=" O ALA A 717 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N VAL A 723 " --> pdb=" O ALA A 719 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N SER A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) 245 hydrogen bonds defined for protein. 729 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.85 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1059 1.34 - 1.46: 883 1.46 - 1.58: 1526 1.58 - 1.70: 1 1.70 - 1.82: 28 Bond restraints: 3497 Sorted by residual: bond pdb=" C11 S1P A 801 " pdb=" C12 S1P A 801 " ideal model delta sigma weight residual 1.573 1.523 0.050 2.00e-02 2.50e+03 6.21e+00 bond pdb=" C12 S1P A 801 " pdb=" C13 S1P A 801 " ideal model delta sigma weight residual 1.569 1.523 0.046 2.00e-02 2.50e+03 5.26e+00 bond pdb=" C13 S1P A 801 " pdb=" C14 S1P A 801 " ideal model delta sigma weight residual 1.569 1.524 0.045 2.00e-02 2.50e+03 5.00e+00 bond pdb=" N MET A 426 " pdb=" CA MET A 426 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.19e-02 7.06e+03 3.69e+00 bond pdb=" C10 S1P A 801 " pdb=" C11 S1P A 801 " ideal model delta sigma weight residual 1.562 1.524 0.038 2.00e-02 2.50e+03 3.60e+00 ... (remaining 3492 not shown) Histogram of bond angle deviations from ideal: 99.97 - 106.77: 75 106.77 - 113.58: 1954 113.58 - 120.38: 1371 120.38 - 127.19: 1309 127.19 - 134.00: 37 Bond angle restraints: 4746 Sorted by residual: angle pdb=" C PHE A 177 " pdb=" N TRP A 178 " pdb=" CA TRP A 178 " ideal model delta sigma weight residual 120.68 114.31 6.37 1.70e+00 3.46e-01 1.41e+01 angle pdb=" N GLN A 659 " pdb=" CA GLN A 659 " pdb=" C GLN A 659 " ideal model delta sigma weight residual 111.11 107.31 3.80 1.20e+00 6.94e-01 1.00e+01 angle pdb=" N ILE A 565 " pdb=" CA ILE A 565 " pdb=" CB ILE A 565 " ideal model delta sigma weight residual 110.54 114.76 -4.22 1.36e+00 5.41e-01 9.61e+00 angle pdb=" CA TRP A 178 " pdb=" CB TRP A 178 " pdb=" CG TRP A 178 " ideal model delta sigma weight residual 113.60 119.40 -5.80 1.90e+00 2.77e-01 9.33e+00 angle pdb=" CB MET A 467 " pdb=" CG MET A 467 " pdb=" SD MET A 467 " ideal model delta sigma weight residual 112.70 121.50 -8.80 3.00e+00 1.11e-01 8.60e+00 ... (remaining 4741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 1950 35.05 - 70.09: 70 70.09 - 105.14: 4 105.14 - 140.19: 0 140.19 - 175.23: 1 Dihedral angle restraints: 2025 sinusoidal: 760 harmonic: 1265 Sorted by residual: dihedral pdb=" C11 S1P A 801 " pdb=" C10 S1P A 801 " pdb=" C9 S1P A 801 " pdb=" C8 S1P A 801 " ideal model delta sinusoidal sigma weight residual 241.31 66.08 175.23 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA CYS A 549 " pdb=" CB CYS A 549 " pdb=" SG CYS A 549 " pdb=" SG CYS A 554 " ideal model delta sinusoidal sigma weight residual 79.00 4.98 74.02 1 2.00e+01 2.50e-03 1.74e+01 dihedral pdb=" C6 S1P A 801 " pdb=" C7 S1P A 801 " pdb=" C8 S1P A 801 " pdb=" C9 S1P A 801 " ideal model delta sinusoidal sigma weight residual -139.76 -41.51 -98.25 1 3.00e+01 1.11e-03 1.22e+01 ... (remaining 2022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 429 0.046 - 0.092: 103 0.092 - 0.138: 19 0.138 - 0.183: 3 0.183 - 0.229: 1 Chirality restraints: 555 Sorted by residual: chirality pdb=" CB THR A 444 " pdb=" CA THR A 444 " pdb=" OG1 THR A 444 " pdb=" CG2 THR A 444 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB ILE A 565 " pdb=" CA ILE A 565 " pdb=" CG1 ILE A 565 " pdb=" CG2 ILE A 565 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" CB THR A 630 " pdb=" CA THR A 630 " pdb=" OG1 THR A 630 " pdb=" CG2 THR A 630 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.20e-01 ... (remaining 552 not shown) Planarity restraints: 584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 178 " -0.029 2.00e-02 2.50e+03 2.33e-02 1.36e+01 pdb=" CG TRP A 178 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 178 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 178 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 178 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 178 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 178 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 178 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 178 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 178 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 552 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO A 553 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 553 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 553 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 658 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.97e+00 pdb=" C LEU A 658 " -0.024 2.00e-02 2.50e+03 pdb=" O LEU A 658 " 0.009 2.00e-02 2.50e+03 pdb=" N GLN A 659 " 0.008 2.00e-02 2.50e+03 ... (remaining 581 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 266 2.74 - 3.28: 3590 3.28 - 3.82: 5763 3.82 - 4.36: 6037 4.36 - 4.90: 10781 Nonbonded interactions: 26437 Sorted by model distance: nonbonded pdb=" OE1 GLN A 543 " pdb=" OG1 THR A 545 " model vdw 2.196 2.440 nonbonded pdb=" ND2 ASN A 115 " pdb=" OE1 GLU A 207 " model vdw 2.205 2.520 nonbonded pdb=" O ILE A 443 " pdb=" OG SER A 447 " model vdw 2.262 2.440 nonbonded pdb=" OG SER A 145 " pdb=" O ALA A 669 " model vdw 2.331 2.440 nonbonded pdb=" N ASP A 668 " pdb=" OD1 ASP A 668 " model vdw 2.345 2.520 ... (remaining 26432 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 4.980 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.040 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 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 : 0.004 0.052 3497 Z= 0.238 Angle : 0.594 8.798 4746 Z= 0.322 Chirality : 0.041 0.229 555 Planarity : 0.004 0.049 584 Dihedral : 17.860 175.234 1214 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 30.06 % Favored : 69.94 % 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: 1.50 (0.42), residues: 442 helix: 1.63 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -1.52 (0.75), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP A 178 HIS 0.003 0.001 HIS A 484 PHE 0.023 0.001 PHE A 222 TYR 0.018 0.001 TYR A 645 ARG 0.003 0.000 ARG A 726 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.338 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1198 time to fit residues: 9.7026 Evaluate side-chains 59 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 0.0010 chunk 34 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 39 optimal weight: 0.0050 overall best weight: 0.4400 ------------------------------------------------------------------------------- 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: 0.8292 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3497 Z= 0.162 Angle : 0.529 7.724 4746 Z= 0.274 Chirality : 0.038 0.160 555 Planarity : 0.004 0.050 584 Dihedral : 10.256 173.804 496 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.21 % Allowed : 25.28 % Favored : 70.51 % 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: 2.26 (0.42), residues: 442 helix: 2.30 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -2.05 (0.71), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 178 HIS 0.002 0.001 HIS A 664 PHE 0.013 0.001 PHE A 523 TYR 0.015 0.001 TYR A 645 ARG 0.003 0.000 ARG A 726 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8763 (mp) REVERT: A 440 LEU cc_start: 0.9120 (mt) cc_final: 0.8914 (mm) outliers start: 15 outliers final: 10 residues processed: 70 average time/residue: 0.1070 time to fit residues: 10.0735 Evaluate side-chains 69 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 718 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 35 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.8353 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3497 Z= 0.205 Angle : 0.540 6.973 4746 Z= 0.282 Chirality : 0.039 0.185 555 Planarity : 0.003 0.049 584 Dihedral : 10.254 174.906 496 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.62 % Allowed : 26.40 % Favored : 67.98 % 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: 2.34 (0.41), residues: 442 helix: 2.42 (0.27), residues: 350 sheet: None (None), residues: 0 loop : -2.12 (0.67), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 178 HIS 0.002 0.001 HIS A 456 PHE 0.013 0.001 PHE A 523 TYR 0.019 0.001 TYR A 160 ARG 0.003 0.000 ARG A 726 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 57 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 115 ASN cc_start: 0.8830 (OUTLIER) cc_final: 0.7373 (t0) REVERT: A 161 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8827 (mp) REVERT: A 192 TYR cc_start: 0.7917 (m-80) cc_final: 0.7565 (m-80) REVERT: A 207 GLU cc_start: 0.8535 (mm-30) cc_final: 0.7561 (mm-30) REVERT: A 440 LEU cc_start: 0.9184 (mt) cc_final: 0.8957 (mm) REVERT: A 543 GLN cc_start: 0.7761 (tm-30) cc_final: 0.7460 (tm-30) outliers start: 20 outliers final: 15 residues processed: 70 average time/residue: 0.1086 time to fit residues: 10.0846 Evaluate side-chains 72 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 55 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 173 CYS Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 718 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8363 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3497 Z= 0.210 Angle : 0.543 8.115 4746 Z= 0.283 Chirality : 0.039 0.194 555 Planarity : 0.004 0.050 584 Dihedral : 10.321 179.939 496 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.90 % Allowed : 26.69 % Favored : 67.42 % 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: 2.36 (0.41), residues: 442 helix: 2.40 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -2.16 (0.68), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 178 HIS 0.002 0.001 HIS A 537 PHE 0.013 0.001 PHE A 523 TYR 0.017 0.001 TYR A 645 ARG 0.002 0.000 ARG A 726 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 59 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8405 (t0) REVERT: A 161 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8829 (mp) REVERT: A 192 TYR cc_start: 0.7920 (m-80) cc_final: 0.7668 (m-80) REVERT: A 543 GLN cc_start: 0.7751 (tm-30) cc_final: 0.7411 (tm-30) outliers start: 21 outliers final: 15 residues processed: 73 average time/residue: 0.1109 time to fit residues: 10.7133 Evaluate side-chains 72 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 55 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 718 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 21 optimal weight: 0.1980 chunk 38 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3497 Z= 0.161 Angle : 0.512 6.522 4746 Z= 0.268 Chirality : 0.038 0.195 555 Planarity : 0.003 0.048 584 Dihedral : 10.127 176.693 496 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 5.62 % Allowed : 26.69 % Favored : 67.70 % 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: 2.50 (0.42), residues: 442 helix: 2.50 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -2.09 (0.69), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 178 HIS 0.001 0.000 HIS A 537 PHE 0.013 0.001 PHE A 523 TYR 0.020 0.001 TYR A 160 ARG 0.003 0.000 ARG A 726 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 62 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 115 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.7571 (t0) REVERT: A 161 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8764 (mp) REVERT: A 192 TYR cc_start: 0.7818 (m-80) cc_final: 0.7612 (m-80) REVERT: A 207 GLU cc_start: 0.8494 (mm-30) cc_final: 0.7856 (mm-30) REVERT: A 633 PHE cc_start: 0.8588 (m-10) cc_final: 0.8209 (m-10) REVERT: A 652 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8263 (mtm180) outliers start: 20 outliers final: 12 residues processed: 74 average time/residue: 0.1390 time to fit residues: 13.1227 Evaluate side-chains 70 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 55 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 718 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 19 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3497 Z= 0.205 Angle : 0.556 7.320 4746 Z= 0.291 Chirality : 0.039 0.207 555 Planarity : 0.004 0.050 584 Dihedral : 9.921 171.566 496 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 5.62 % Allowed : 26.97 % Favored : 67.42 % 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: 2.46 (0.42), residues: 442 helix: 2.48 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -2.16 (0.69), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 178 HIS 0.002 0.001 HIS A 456 PHE 0.013 0.001 PHE A 523 TYR 0.019 0.001 TYR A 645 ARG 0.004 0.000 ARG A 726 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 59 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 115 ASN cc_start: 0.8783 (OUTLIER) cc_final: 0.7652 (t0) REVERT: A 207 GLU cc_start: 0.8524 (mm-30) cc_final: 0.7910 (mm-30) REVERT: A 633 PHE cc_start: 0.8612 (m-10) cc_final: 0.8103 (m-10) REVERT: A 652 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8324 (mtm180) outliers start: 20 outliers final: 16 residues processed: 73 average time/residue: 0.1219 time to fit residues: 11.5328 Evaluate side-chains 77 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 59 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 718 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 25 optimal weight: 0.0770 chunk 19 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3497 Z= 0.185 Angle : 0.544 7.499 4746 Z= 0.285 Chirality : 0.039 0.216 555 Planarity : 0.004 0.048 584 Dihedral : 9.851 167.881 496 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 6.74 % Allowed : 26.12 % Favored : 67.13 % 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: 2.54 (0.42), residues: 442 helix: 2.50 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -1.93 (0.71), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 178 HIS 0.002 0.001 HIS A 537 PHE 0.013 0.001 PHE A 523 TYR 0.021 0.001 TYR A 160 ARG 0.004 0.000 ARG A 726 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 59 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 115 ASN cc_start: 0.8758 (OUTLIER) cc_final: 0.7698 (t0) REVERT: A 207 GLU cc_start: 0.8511 (mm-30) cc_final: 0.7944 (mm-30) REVERT: A 652 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8311 (mtm180) outliers start: 24 outliers final: 18 residues processed: 75 average time/residue: 0.1273 time to fit residues: 12.4158 Evaluate side-chains 78 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 58 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 718 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 8.9990 chunk 3 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 0.0980 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 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 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3497 Z= 0.189 Angle : 0.551 8.232 4746 Z= 0.290 Chirality : 0.040 0.218 555 Planarity : 0.004 0.050 584 Dihedral : 9.689 161.359 496 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 6.18 % Allowed : 26.12 % Favored : 67.70 % 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: 2.51 (0.42), residues: 442 helix: 2.49 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -1.94 (0.71), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 178 HIS 0.002 0.001 HIS A 537 PHE 0.012 0.001 PHE A 523 TYR 0.017 0.001 TYR A 645 ARG 0.003 0.000 ARG A 726 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 58 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 115 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.7714 (t0) REVERT: A 207 GLU cc_start: 0.8524 (mm-30) cc_final: 0.7968 (mm-30) REVERT: A 652 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8314 (mtm180) outliers start: 22 outliers final: 18 residues processed: 72 average time/residue: 0.1250 time to fit residues: 11.5472 Evaluate side-chains 78 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 58 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 718 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 19 optimal weight: 0.0170 chunk 29 optimal weight: 0.0870 chunk 43 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 3497 Z= 0.172 Angle : 0.558 9.636 4746 Z= 0.291 Chirality : 0.040 0.223 555 Planarity : 0.004 0.049 584 Dihedral : 9.531 156.551 496 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.62 % Allowed : 27.25 % Favored : 67.13 % 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: 2.55 (0.42), residues: 442 helix: 2.48 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -1.80 (0.72), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 178 HIS 0.001 0.000 HIS A 537 PHE 0.012 0.001 PHE A 626 TYR 0.024 0.001 TYR A 160 ARG 0.004 0.000 ARG A 726 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 59 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 115 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.7713 (t0) REVERT: A 207 GLU cc_start: 0.8509 (mm-30) cc_final: 0.7993 (mm-30) REVERT: A 652 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8326 (mtm180) outliers start: 20 outliers final: 17 residues processed: 72 average time/residue: 0.1244 time to fit residues: 11.6208 Evaluate side-chains 77 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 58 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 718 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.0030 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 3497 Z= 0.202 Angle : 0.605 12.029 4746 Z= 0.306 Chirality : 0.041 0.233 555 Planarity : 0.004 0.051 584 Dihedral : 9.231 144.392 496 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 5.90 % Allowed : 27.25 % Favored : 66.85 % 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: 2.52 (0.42), residues: 442 helix: 2.47 (0.28), residues: 353 sheet: None (None), residues: 0 loop : -1.84 (0.71), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 178 HIS 0.001 0.000 HIS A 537 PHE 0.014 0.001 PHE A 626 TYR 0.025 0.002 TYR A 645 ARG 0.003 0.000 ARG A 726 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 57 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 115 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.7719 (t0) REVERT: A 207 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8009 (mm-30) REVERT: A 633 PHE cc_start: 0.8537 (m-80) cc_final: 0.8069 (m-10) REVERT: A 652 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8342 (mtm180) outliers start: 21 outliers final: 16 residues processed: 72 average time/residue: 0.1235 time to fit residues: 11.6996 Evaluate side-chains 74 residues out of total 356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 56 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 TRP Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 718 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.148406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.112300 restraints weight = 4750.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.116575 restraints weight = 2626.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.119082 restraints weight = 1853.912| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 3497 Z= 0.231 Angle : 0.621 11.390 4746 Z= 0.317 Chirality : 0.041 0.228 555 Planarity : 0.004 0.049 584 Dihedral : 6.787 75.989 496 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.62 % Allowed : 27.25 % Favored : 67.13 % 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: 2.41 (0.42), residues: 442 helix: 2.41 (0.28), residues: 353 sheet: None (None), residues: 0 loop : -1.94 (0.71), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 178 HIS 0.002 0.001 HIS A 537 PHE 0.015 0.001 PHE A 626 TYR 0.008 0.001 TYR A 116 ARG 0.004 0.000 ARG A 726 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1061.21 seconds wall clock time: 19 minutes 52.90 seconds (1192.90 seconds total)