Starting phenix.real_space_refine on Tue Mar 11 15:03:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f0l_50113/03_2025/9f0l_50113_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f0l_50113/03_2025/9f0l_50113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f0l_50113/03_2025/9f0l_50113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f0l_50113/03_2025/9f0l_50113.map" model { file = "/net/cci-nas-00/data/ceres_data/9f0l_50113/03_2025/9f0l_50113_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f0l_50113/03_2025/9f0l_50113_neut.cif" } resolution = 2.76 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= 0.012 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: 3 Type Number sf(0) Gaussians C 3952 2.51 5 N 1064 2.21 5 O 1103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6119 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 6119 Classifications: {'peptide': 791} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 33, 'TRANS': 757} Chain breaks: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 19, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 130 Time building chain proxies: 3.64, per 1000 atoms: 0.59 Number of scatterers: 6119 At special positions: 0 Unit cell: (88.92, 78.66, 112.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1103 8.00 N 1064 7.00 C 3952 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 - 3.00 Amino acid : True - 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: 1.42 Conformation dependent library (CDL) restraints added in 798.1 milliseconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1524 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 1 sheets defined 83.7% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 147 through 169 removed outlier: 3.529A pdb=" N VAL A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 191 removed outlier: 3.807A pdb=" N GLU A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 221 Processing helix chain 'A' and resid 224 through 240 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 284 through 295 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 301 through 329 Processing helix chain 'A' and resid 333 through 353 Processing helix chain 'A' and resid 355 through 372 Processing helix chain 'A' and resid 374 through 408 Processing helix chain 'A' and resid 409 through 429 removed outlier: 3.558A pdb=" N LYS A 413 " --> pdb=" O ASP A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 439 Processing helix chain 'A' and resid 440 through 459 Processing helix chain 'A' and resid 473 through 492 Processing helix chain 'A' and resid 494 through 510 removed outlier: 3.814A pdb=" N ALA A 498 " --> pdb=" O ASP A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 524 Processing helix chain 'A' and resid 527 through 549 removed outlier: 3.791A pdb=" N LEU A 531 " --> pdb=" O SER A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 586 removed outlier: 3.667A pdb=" N LEU A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU A 567 " --> pdb=" O GLU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 620 removed outlier: 3.862A pdb=" N ILE A 620 " --> pdb=" O GLU A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 624 Processing helix chain 'A' and resid 625 through 644 Processing helix chain 'A' and resid 648 through 663 removed outlier: 3.555A pdb=" N PHE A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 656 " --> pdb=" O LEU A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 686 Processing helix chain 'A' and resid 688 through 704 removed outlier: 3.788A pdb=" N VAL A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG A 698 " --> pdb=" O GLU A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 731 removed outlier: 3.591A pdb=" N LEU A 715 " --> pdb=" O GLU A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 743 through 747 removed outlier: 3.883A pdb=" N ILE A 747 " --> pdb=" O PRO A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 811 Processing helix chain 'A' and resid 817 through 850 Processing helix chain 'A' and resid 856 through 875 Processing helix chain 'A' and resid 879 through 885 Processing helix chain 'A' and resid 886 through 901 Processing helix chain 'A' and resid 906 through 922 removed outlier: 3.617A pdb=" N GLU A 911 " --> pdb=" O PRO A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 940 Processing sheet with id=AA1, first strand: chain 'A' and resid 463 through 468 520 hydrogen bonds defined for protein. 1545 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: 1.76 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 1038 1.29 - 1.36: 1039 1.36 - 1.42: 435 1.42 - 1.49: 926 1.49 - 1.55: 2783 Bond restraints: 6221 Sorted by residual: bond pdb=" CB GLU A 616 " pdb=" CG GLU A 616 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.02e+00 bond pdb=" CG1 ILE A 658 " pdb=" CD1 ILE A 658 " ideal model delta sigma weight residual 1.513 1.476 0.037 3.90e-02 6.57e+02 9.05e-01 bond pdb=" CA GLU A 616 " pdb=" CB GLU A 616 " ideal model delta sigma weight residual 1.529 1.542 -0.013 1.78e-02 3.16e+03 5.42e-01 bond pdb=" CG LYS A 762 " pdb=" CD LYS A 762 " ideal model delta sigma weight residual 1.520 1.500 0.020 3.00e-02 1.11e+03 4.53e-01 bond pdb=" N GLU A 616 " pdb=" CA GLU A 616 " ideal model delta sigma weight residual 1.457 1.466 -0.009 1.35e-02 5.49e+03 4.40e-01 ... (remaining 6216 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 8307 1.23 - 2.47: 95 2.47 - 3.70: 34 3.70 - 4.93: 6 4.93 - 6.16: 6 Bond angle restraints: 8448 Sorted by residual: angle pdb=" C ILE A 615 " pdb=" N GLU A 616 " pdb=" CA GLU A 616 " ideal model delta sigma weight residual 121.18 115.65 5.53 1.98e+00 2.55e-01 7.80e+00 angle pdb=" CB GLU A 616 " pdb=" CG GLU A 616 " pdb=" CD GLU A 616 " ideal model delta sigma weight residual 112.60 116.71 -4.11 1.70e+00 3.46e-01 5.83e+00 angle pdb=" CA GLU A 616 " pdb=" CB GLU A 616 " pdb=" CG GLU A 616 " ideal model delta sigma weight residual 114.10 118.88 -4.78 2.00e+00 2.50e-01 5.71e+00 angle pdb=" N GLU A 616 " pdb=" CA GLU A 616 " pdb=" CB GLU A 616 " ideal model delta sigma weight residual 110.39 114.52 -4.13 1.75e+00 3.27e-01 5.57e+00 angle pdb=" N GLY A 776 " pdb=" CA GLY A 776 " pdb=" C GLY A 776 " ideal model delta sigma weight residual 113.18 118.08 -4.90 2.37e+00 1.78e-01 4.27e+00 ... (remaining 8443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 3232 17.67 - 35.34: 407 35.34 - 53.00: 133 53.00 - 70.67: 32 70.67 - 88.34: 11 Dihedral angle restraints: 3815 sinusoidal: 1484 harmonic: 2331 Sorted by residual: dihedral pdb=" CG ARG A 784 " pdb=" CD ARG A 784 " pdb=" NE ARG A 784 " pdb=" CZ ARG A 784 " ideal model delta sinusoidal sigma weight residual 180.00 135.04 44.96 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CA GLU A 867 " pdb=" C GLU A 867 " pdb=" N SER A 868 " pdb=" CA SER A 868 " ideal model delta harmonic sigma weight residual 180.00 163.73 16.27 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CG ARG A 690 " pdb=" CD ARG A 690 " pdb=" NE ARG A 690 " pdb=" CZ ARG A 690 " ideal model delta sinusoidal sigma weight residual 90.00 134.64 -44.64 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 3812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 791 0.037 - 0.074: 162 0.074 - 0.111: 41 0.111 - 0.148: 8 0.148 - 0.185: 3 Chirality restraints: 1005 Sorted by residual: chirality pdb=" CA GLU A 616 " pdb=" N GLU A 616 " pdb=" C GLU A 616 " pdb=" CB GLU A 616 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.54e-01 chirality pdb=" CA GLU A 867 " pdb=" N GLU A 867 " pdb=" C GLU A 867 " pdb=" CB GLU A 867 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CB ILE A 636 " pdb=" CA ILE A 636 " pdb=" CG1 ILE A 636 " pdb=" CG2 ILE A 636 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.94e-01 ... (remaining 1002 not shown) Planarity restraints: 1094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 867 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.51e+00 pdb=" C GLU A 867 " -0.027 2.00e-02 2.50e+03 pdb=" O GLU A 867 " 0.010 2.00e-02 2.50e+03 pdb=" N SER A 868 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 779 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO A 780 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 780 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 780 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 185 " 0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO A 186 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 186 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 186 " 0.020 5.00e-02 4.00e+02 ... (remaining 1091 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1424 2.80 - 3.32: 6073 3.32 - 3.85: 10636 3.85 - 4.37: 11927 4.37 - 4.90: 21156 Nonbonded interactions: 51216 Sorted by model distance: nonbonded pdb=" OH TYR A 491 " pdb=" OD1 ASP A 536 " model vdw 2.271 3.040 nonbonded pdb=" O ILE A 332 " pdb=" NE2 GLN A 337 " model vdw 2.307 3.120 nonbonded pdb=" OD1 ASP A 425 " pdb=" NH2 ARG A 778 " model vdw 2.340 3.120 nonbonded pdb=" O LEU A 426 " pdb=" OG1 THR A 432 " model vdw 2.365 3.040 nonbonded pdb=" NE2 GLN A 545 " pdb=" OD1 ASP A 553 " model vdw 2.393 3.120 ... (remaining 51211 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.940 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:10.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 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 : 0.002 0.037 6221 Z= 0.136 Angle : 0.433 6.163 8448 Z= 0.222 Chirality : 0.035 0.185 1005 Planarity : 0.004 0.039 1094 Dihedral : 18.236 88.336 2291 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 0.84 % Allowed : 28.86 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.17 (0.29), residues: 787 helix: 2.22 (0.19), residues: 631 sheet: 1.43 (1.15), residues: 23 loop : 1.84 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 702 HIS 0.002 0.001 HIS A 155 PHE 0.015 0.001 PHE A 654 TYR 0.005 0.001 TYR A 504 ARG 0.005 0.000 ARG A 763 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.723 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 32 average time/residue: 0.9419 time to fit residues: 32.7493 Evaluate side-chains 18 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 730 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.0020 chunk 59 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 40 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 GLN ** A 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.099269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.078029 restraints weight = 11402.535| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.08 r_work: 0.3066 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6221 Z= 0.160 Angle : 0.436 6.424 8448 Z= 0.229 Chirality : 0.035 0.161 1005 Planarity : 0.004 0.051 1094 Dihedral : 3.675 45.644 883 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 4.03 % Allowed : 24.50 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.81 (0.28), residues: 787 helix: 2.70 (0.19), residues: 641 sheet: 1.61 (1.18), residues: 23 loop : 1.83 (0.61), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 702 HIS 0.002 0.001 HIS A 155 PHE 0.021 0.001 PHE A 165 TYR 0.007 0.001 TYR A 309 ARG 0.002 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 20 time to evaluate : 0.673 Fit side-chains REVERT: A 490 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8186 (tm-30) REVERT: A 656 SER cc_start: 0.8097 (OUTLIER) cc_final: 0.7820 (t) REVERT: A 844 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8044 (tp) outliers start: 24 outliers final: 6 residues processed: 41 average time/residue: 0.9069 time to fit residues: 40.3355 Evaluate side-chains 22 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 13 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 848 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.0770 chunk 71 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 ASN ** A 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.098240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.077108 restraints weight = 11534.180| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.08 r_work: 0.3045 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6221 Z= 0.171 Angle : 0.431 6.557 8448 Z= 0.223 Chirality : 0.035 0.184 1005 Planarity : 0.004 0.048 1094 Dihedral : 3.401 45.203 879 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 3.52 % Allowed : 24.33 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.98 (0.28), residues: 787 helix: 2.83 (0.19), residues: 639 sheet: 1.70 (1.22), residues: 23 loop : 1.83 (0.60), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 702 HIS 0.001 0.001 HIS A 719 PHE 0.020 0.001 PHE A 165 TYR 0.005 0.001 TYR A 323 ARG 0.003 0.000 ARG A 678 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 18 time to evaluate : 0.571 Fit side-chains REVERT: A 490 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8195 (tm-30) REVERT: A 656 SER cc_start: 0.8107 (OUTLIER) cc_final: 0.7852 (t) REVERT: A 933 GLU cc_start: 0.8175 (tp30) cc_final: 0.7953 (tp30) outliers start: 21 outliers final: 9 residues processed: 35 average time/residue: 0.6938 time to fit residues: 27.0857 Evaluate side-chains 26 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 15 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 848 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 40 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 GLN A 586 ASN A 706 GLN ** A 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.096954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.075771 restraints weight = 11658.297| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 3.10 r_work: 0.3019 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6221 Z= 0.188 Angle : 0.434 6.559 8448 Z= 0.223 Chirality : 0.036 0.180 1005 Planarity : 0.004 0.048 1094 Dihedral : 3.398 46.136 879 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.52 % Allowed : 25.00 % Favored : 71.48 % 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: 4.06 (0.28), residues: 787 helix: 2.88 (0.19), residues: 639 sheet: 1.77 (1.23), residues: 23 loop : 1.88 (0.60), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 871 HIS 0.002 0.001 HIS A 719 PHE 0.021 0.001 PHE A 165 TYR 0.007 0.001 TYR A 520 ARG 0.002 0.000 ARG A 678 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 18 time to evaluate : 0.693 Fit side-chains REVERT: A 490 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8206 (tm-30) REVERT: A 656 SER cc_start: 0.8162 (OUTLIER) cc_final: 0.7908 (t) REVERT: A 933 GLU cc_start: 0.8204 (tp30) cc_final: 0.7896 (tp30) outliers start: 21 outliers final: 9 residues processed: 36 average time/residue: 0.7404 time to fit residues: 29.5759 Evaluate side-chains 27 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 16 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 761 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 48 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 ASN ** A 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.096131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.074941 restraints weight = 11672.739| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.11 r_work: 0.3006 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6221 Z= 0.206 Angle : 0.441 6.672 8448 Z= 0.225 Chirality : 0.036 0.179 1005 Planarity : 0.004 0.049 1094 Dihedral : 3.426 46.555 879 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 3.19 % Allowed : 24.66 % Favored : 72.15 % 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: 4.09 (0.28), residues: 787 helix: 2.91 (0.19), residues: 637 sheet: 1.72 (1.25), residues: 23 loop : 1.83 (0.58), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 860 HIS 0.002 0.001 HIS A 719 PHE 0.022 0.001 PHE A 165 TYR 0.007 0.001 TYR A 520 ARG 0.002 0.000 ARG A 678 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 13 time to evaluate : 0.575 Fit side-chains REVERT: A 490 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8229 (tm-30) REVERT: A 656 SER cc_start: 0.8190 (OUTLIER) cc_final: 0.7941 (t) REVERT: A 933 GLU cc_start: 0.8170 (tp30) cc_final: 0.7909 (tp30) outliers start: 19 outliers final: 9 residues processed: 30 average time/residue: 1.0391 time to fit residues: 33.7190 Evaluate side-chains 24 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 13 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 761 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 64 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 ASN ** A 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.095793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.074713 restraints weight = 11604.634| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.09 r_work: 0.3008 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6221 Z= 0.213 Angle : 0.443 6.767 8448 Z= 0.226 Chirality : 0.036 0.179 1005 Planarity : 0.004 0.048 1094 Dihedral : 3.434 47.122 879 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.52 % Allowed : 24.16 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.07 (0.28), residues: 787 helix: 2.89 (0.19), residues: 639 sheet: 1.64 (1.23), residues: 23 loop : 1.88 (0.59), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 317 HIS 0.002 0.001 HIS A 719 PHE 0.025 0.001 PHE A 165 TYR 0.006 0.001 TYR A 520 ARG 0.004 0.000 ARG A 914 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 14 time to evaluate : 0.686 Fit side-chains REVERT: A 490 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8221 (tm-30) REVERT: A 656 SER cc_start: 0.8249 (OUTLIER) cc_final: 0.7996 (t) REVERT: A 933 GLU cc_start: 0.8164 (tp30) cc_final: 0.7889 (tp30) outliers start: 21 outliers final: 10 residues processed: 34 average time/residue: 0.9218 time to fit residues: 34.3595 Evaluate side-chains 25 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 13 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 848 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 55 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 chunk 73 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 GLN A 586 ASN ** A 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.096206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.075104 restraints weight = 11611.195| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.10 r_work: 0.3011 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6221 Z= 0.190 Angle : 0.436 6.668 8448 Z= 0.222 Chirality : 0.036 0.195 1005 Planarity : 0.004 0.048 1094 Dihedral : 3.452 46.629 879 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.68 % Allowed : 24.83 % Favored : 72.48 % 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: 4.11 (0.28), residues: 787 helix: 2.92 (0.19), residues: 639 sheet: 1.59 (1.23), residues: 23 loop : 1.91 (0.60), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 860 HIS 0.002 0.001 HIS A 719 PHE 0.026 0.002 PHE A 165 TYR 0.006 0.001 TYR A 520 ARG 0.003 0.000 ARG A 914 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 15 time to evaluate : 0.654 Fit side-chains REVERT: A 490 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8230 (tm-30) REVERT: A 656 SER cc_start: 0.8297 (OUTLIER) cc_final: 0.8050 (t) REVERT: A 933 GLU cc_start: 0.8224 (tp30) cc_final: 0.7975 (tp30) outliers start: 16 outliers final: 11 residues processed: 29 average time/residue: 0.5868 time to fit residues: 19.6581 Evaluate side-chains 28 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 15 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 848 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 54 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 ASN ** A 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.096409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.075289 restraints weight = 11527.102| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.09 r_work: 0.3021 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6221 Z= 0.183 Angle : 0.445 8.948 8448 Z= 0.223 Chirality : 0.035 0.191 1005 Planarity : 0.004 0.048 1094 Dihedral : 3.430 46.414 879 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.52 % Allowed : 25.17 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.14 (0.28), residues: 787 helix: 2.94 (0.18), residues: 639 sheet: 1.57 (1.22), residues: 23 loop : 1.93 (0.60), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 860 HIS 0.002 0.001 HIS A 719 PHE 0.027 0.001 PHE A 165 TYR 0.008 0.001 TYR A 520 ARG 0.003 0.000 ARG A 914 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 16 time to evaluate : 0.653 Fit side-chains REVERT: A 402 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8442 (tm-30) REVERT: A 490 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8207 (tm-30) REVERT: A 656 SER cc_start: 0.8312 (OUTLIER) cc_final: 0.8071 (t) REVERT: A 933 GLU cc_start: 0.8188 (tp30) cc_final: 0.7905 (tp30) outliers start: 15 outliers final: 12 residues processed: 29 average time/residue: 0.7632 time to fit residues: 24.7646 Evaluate side-chains 30 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 15 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 848 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 14 optimal weight: 0.0000 chunk 41 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 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 = 0.3606 r_free = 0.3606 target = 0.098136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.077671 restraints weight = 11681.164| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.98 r_work: 0.3061 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6221 Z= 0.207 Angle : 0.461 8.077 8448 Z= 0.232 Chirality : 0.036 0.194 1005 Planarity : 0.004 0.048 1094 Dihedral : 3.451 46.915 879 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.68 % Allowed : 25.17 % Favored : 72.15 % 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: 4.13 (0.28), residues: 787 helix: 2.92 (0.19), residues: 639 sheet: 1.58 (1.23), residues: 23 loop : 1.99 (0.60), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 317 HIS 0.002 0.001 HIS A 719 PHE 0.027 0.002 PHE A 165 TYR 0.009 0.001 TYR A 520 ARG 0.002 0.000 ARG A 914 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 15 time to evaluate : 0.700 Fit side-chains REVERT: A 402 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8540 (tm-30) REVERT: A 473 ASN cc_start: 0.8623 (t0) cc_final: 0.8321 (t0) REVERT: A 490 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8349 (tm-30) REVERT: A 656 SER cc_start: 0.8547 (OUTLIER) cc_final: 0.8319 (t) REVERT: A 933 GLU cc_start: 0.8290 (tp30) cc_final: 0.8032 (tp30) outliers start: 16 outliers final: 10 residues processed: 29 average time/residue: 0.5600 time to fit residues: 18.9367 Evaluate side-chains 28 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 15 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 848 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 47 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 46 optimal weight: 0.1980 chunk 45 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 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 = 0.3618 r_free = 0.3618 target = 0.099053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.078607 restraints weight = 11673.164| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.00 r_work: 0.3080 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6221 Z= 0.170 Angle : 0.447 8.223 8448 Z= 0.225 Chirality : 0.035 0.185 1005 Planarity : 0.004 0.048 1094 Dihedral : 3.420 45.898 879 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.18 % Allowed : 26.01 % Favored : 71.81 % 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: 4.17 (0.28), residues: 787 helix: 2.95 (0.19), residues: 639 sheet: 1.53 (1.21), residues: 23 loop : 2.02 (0.61), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 860 HIS 0.002 0.001 HIS A 719 PHE 0.028 0.001 PHE A 165 TYR 0.007 0.001 TYR A 520 ARG 0.002 0.000 ARG A 914 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 18 time to evaluate : 0.667 Fit side-chains REVERT: A 402 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8551 (tm-30) REVERT: A 473 ASN cc_start: 0.8617 (t0) cc_final: 0.8318 (t0) REVERT: A 490 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8329 (tm-30) REVERT: A 656 SER cc_start: 0.8582 (OUTLIER) cc_final: 0.8363 (t) REVERT: A 933 GLU cc_start: 0.8390 (tp30) cc_final: 0.8128 (tp30) outliers start: 13 outliers final: 10 residues processed: 30 average time/residue: 0.5953 time to fit residues: 20.3217 Evaluate side-chains 30 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 17 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 848 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 69 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 62 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 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 = 0.3607 r_free = 0.3607 target = 0.098238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.077697 restraints weight = 11705.577| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.01 r_work: 0.3064 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6221 Z= 0.200 Angle : 0.458 8.022 8448 Z= 0.231 Chirality : 0.036 0.191 1005 Planarity : 0.004 0.048 1094 Dihedral : 3.442 46.732 879 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.35 % Allowed : 25.84 % Favored : 71.81 % 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: 4.15 (0.28), residues: 787 helix: 2.93 (0.19), residues: 639 sheet: 1.55 (1.21), residues: 23 loop : 2.02 (0.61), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 317 HIS 0.002 0.001 HIS A 719 PHE 0.028 0.001 PHE A 165 TYR 0.009 0.001 TYR A 520 ARG 0.002 0.000 ARG A 914 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3203.18 seconds wall clock time: 55 minutes 31.05 seconds (3331.05 seconds total)