Starting phenix.real_space_refine on Fri Dec 27 15:11:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c44_16416/12_2024/8c44_16416.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c44_16416/12_2024/8c44_16416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c44_16416/12_2024/8c44_16416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c44_16416/12_2024/8c44_16416.map" model { file = "/net/cci-nas-00/data/ceres_data/8c44_16416/12_2024/8c44_16416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c44_16416/12_2024/8c44_16416.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.061 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 27 5.16 5 C 3363 2.51 5 N 896 2.21 5 O 952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 5239 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3821 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 12, 'TRANS': 445} Chain breaks: 17 Chain: "C" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1354 Classifications: {'peptide': 165} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 158} Chain breaks: 1 Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.74, per 1000 atoms: 0.90 Number of scatterers: 5239 At special positions: 0 Unit cell: (64.064, 74.048, 130.624, 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 27 16.00 P 1 15.00 O 952 8.00 N 896 7.00 C 3363 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 553 " distance=2.07 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 608 " distance=2.04 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 710 " distance=2.03 Simple disulfide: pdb=" SG CYS A1027 " - pdb=" SG CYS A1174 " distance=2.04 Simple disulfide: pdb=" SG CYS C 101 " - pdb=" SG CYS C 169 " distance=2.08 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 Links applied NAG-ASN " NAG C 202 " - " ASN C 47 " Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 611.0 milliseconds 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1192 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 3 sheets defined 62.1% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 571 through 594 Processing helix chain 'A' and resid 606 through 631 Processing helix chain 'A' and resid 646 through 660 removed outlier: 5.447A pdb=" N PHE A 656 " --> pdb=" O ASP A 652 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N GLN A 657 " --> pdb=" O SER A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 683 Processing helix chain 'A' and resid 694 through 715 removed outlier: 3.572A pdb=" N ASN A 713 " --> pdb=" O ILE A 709 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN A 714 " --> pdb=" O CYS A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 763 Processing helix chain 'A' and resid 764 through 769 Processing helix chain 'A' and resid 771 through 775 Processing helix chain 'A' and resid 842 through 847 Processing helix chain 'A' and resid 869 through 892 Processing helix chain 'A' and resid 904 through 924 Processing helix chain 'A' and resid 931 through 950 Processing helix chain 'A' and resid 971 through 982 Processing helix chain 'A' and resid 983 through 990 removed outlier: 3.611A pdb=" N MET A 990 " --> pdb=" O VAL A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1006 removed outlier: 3.985A pdb=" N HIS A1005 " --> pdb=" O SER A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1012 Processing helix chain 'A' and resid 1013 through 1035 Processing helix chain 'A' and resid 1069 through 1096 removed outlier: 3.743A pdb=" N GLN A1077 " --> pdb=" O THR A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1125 Processing helix chain 'A' and resid 1161 through 1170 Processing helix chain 'C' and resid 58 through 87 Processing helix chain 'C' and resid 128 through 131 Processing helix chain 'C' and resid 141 through 154 removed outlier: 3.502A pdb=" N TYR C 154 " --> pdb=" O GLN C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 159 through 167 Processing helix chain 'C' and resid 167 through 176 Processing sheet with id=AA1, first strand: chain 'A' and resid 504 through 506 Processing sheet with id=AA2, first strand: chain 'A' and resid 826 through 828 removed outlier: 3.686A pdb=" N THR A 826 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 49 through 52 removed outlier: 6.647A pdb=" N ALA C 31 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL C 40 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLY C 29 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU C 42 " --> pdb=" O TYR C 27 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TYR C 27 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL C 25 " --> pdb=" O PRO C 44 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N HIS C 24 " --> pdb=" O ARG C 20 " (cutoff:3.500A) removed outlier: 9.801A pdb=" N VAL C 112 " --> pdb=" O ARG C 127 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG C 127 " --> pdb=" O VAL C 112 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N PHE C 114 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER C 125 " --> pdb=" O PHE C 114 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL C 116 " --> pdb=" O PHE C 123 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 948 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: 1.52 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1093 1.32 - 1.46: 1702 1.46 - 1.59: 2499 1.59 - 1.72: 24 1.72 - 1.85: 34 Bond restraints: 5352 Sorted by residual: bond pdb=" C THR A1154 " pdb=" N PRO A1155 " ideal model delta sigma weight residual 1.331 1.396 -0.065 1.31e-02 5.83e+03 2.50e+01 bond pdb=" N VAL C 124 " pdb=" CA VAL C 124 " ideal model delta sigma weight residual 1.459 1.509 -0.050 1.07e-02 8.73e+03 2.17e+01 bond pdb=" C ILE A 639 " pdb=" N PRO A 640 " ideal model delta sigma weight residual 1.330 1.386 -0.056 1.22e-02 6.72e+03 2.13e+01 bond pdb=" N PRO A 640 " pdb=" CD PRO A 640 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.56e+01 bond pdb=" CB ILE A1012 " pdb=" CG1 ILE A1012 " ideal model delta sigma weight residual 1.530 1.451 0.079 2.00e-02 2.50e+03 1.54e+01 ... (remaining 5347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 6977 3.97 - 7.94: 201 7.94 - 11.91: 9 11.91 - 15.88: 0 15.88 - 19.85: 2 Bond angle restraints: 7189 Sorted by residual: angle pdb=" N PRO C 22 " pdb=" CA PRO C 22 " pdb=" C PRO C 22 " ideal model delta sigma weight residual 113.53 102.47 11.06 1.39e+00 5.18e-01 6.33e+01 angle pdb=" C THR A1006 " pdb=" N PRO A1007 " pdb=" CA PRO A1007 " ideal model delta sigma weight residual 120.21 127.27 -7.06 9.60e-01 1.09e+00 5.41e+01 angle pdb=" C ARG C 127 " pdb=" N PRO C 128 " pdb=" CA PRO C 128 " ideal model delta sigma weight residual 119.84 128.85 -9.01 1.25e+00 6.40e-01 5.20e+01 angle pdb=" C GLY C 43 " pdb=" N PRO C 44 " pdb=" CA PRO C 44 " ideal model delta sigma weight residual 120.21 126.84 -6.63 9.60e-01 1.09e+00 4.77e+01 angle pdb=" C THR A 823 " pdb=" N PRO A 824 " pdb=" CA PRO A 824 " ideal model delta sigma weight residual 119.78 126.72 -6.94 1.03e+00 9.43e-01 4.54e+01 ... (remaining 7184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.24: 3152 32.24 - 64.48: 62 64.48 - 96.71: 7 96.71 - 128.95: 0 128.95 - 161.19: 1 Dihedral angle restraints: 3222 sinusoidal: 1394 harmonic: 1828 Sorted by residual: dihedral pdb=" CB CYS A 612 " pdb=" SG CYS A 612 " pdb=" SG CYS A 710 " pdb=" CB CYS A 710 " ideal model delta sinusoidal sigma weight residual -86.00 -174.59 88.59 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" C3 PTY C 201 " pdb=" O11 PTY C 201 " pdb=" P1 PTY C 201 " pdb=" O12 PTY C 201 " ideal model delta sinusoidal sigma weight residual 300.23 139.04 161.19 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" CD ARG C 20 " pdb=" NE ARG C 20 " pdb=" CZ ARG C 20 " pdb=" NH1 ARG C 20 " ideal model delta sinusoidal sigma weight residual 0.00 -36.88 36.88 1 1.00e+01 1.00e-02 1.92e+01 ... (remaining 3219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 519 0.095 - 0.191: 202 0.191 - 0.286: 32 0.286 - 0.381: 1 0.381 - 0.477: 3 Chirality restraints: 757 Sorted by residual: chirality pdb=" CB ILE A 639 " pdb=" CA ILE A 639 " pdb=" CG1 ILE A 639 " pdb=" CG2 ILE A 639 " both_signs ideal model delta sigma weight residual False 2.64 3.12 -0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" C2 NAG C 202 " pdb=" C1 NAG C 202 " pdb=" C3 NAG C 202 " pdb=" N2 NAG C 202 " both_signs ideal model delta sigma weight residual False -2.49 -2.91 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" C1 NAG C 202 " pdb=" ND2 ASN C 47 " pdb=" C2 NAG C 202 " pdb=" O5 NAG C 202 " both_signs ideal model delta sigma weight residual False -2.40 -2.80 0.40 2.00e-01 2.50e+01 4.10e+00 ... (remaining 754 not shown) Planarity restraints: 895 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 20 " 0.647 9.50e-02 1.11e+02 2.90e-01 5.13e+01 pdb=" NE ARG C 20 " -0.039 2.00e-02 2.50e+03 pdb=" CZ ARG C 20 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG C 20 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 20 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1017 " -0.556 9.50e-02 1.11e+02 2.49e-01 3.79e+01 pdb=" NE ARG A1017 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A1017 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A1017 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A1017 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 176 " 0.026 2.00e-02 2.50e+03 5.22e-02 2.72e+01 pdb=" C HIS C 176 " -0.090 2.00e-02 2.50e+03 pdb=" O HIS C 176 " 0.032 2.00e-02 2.50e+03 pdb=" OXT HIS C 176 " 0.032 2.00e-02 2.50e+03 ... (remaining 892 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1746 2.85 - 3.36: 5164 3.36 - 3.87: 9284 3.87 - 4.39: 10847 4.39 - 4.90: 17208 Nonbonded interactions: 44249 Sorted by model distance: nonbonded pdb=" NZ LYS A1015 " pdb=" OD1 ASP A1112 " model vdw 2.336 3.120 nonbonded pdb=" NZ LYS A 745 " pdb=" OD1 ASP A1009 " model vdw 2.388 3.120 nonbonded pdb=" N ASP A 984 " pdb=" OD1 ASP A 984 " model vdw 2.407 3.120 nonbonded pdb=" NZ LYS A 827 " pdb=" OE2 GLU A 838 " model vdw 2.421 3.120 nonbonded pdb=" OD2 ASP A 572 " pdb=" NZ LYS A 642 " model vdw 2.444 3.120 ... (remaining 44244 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 5.160 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.230 Find NCS groups from input model: 0.050 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 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 : 0.020 0.123 5352 Z= 1.243 Angle : 1.659 19.848 7189 Z= 1.122 Chirality : 0.098 0.477 757 Planarity : 0.015 0.290 894 Dihedral : 12.787 161.189 2015 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.54 % Allowed : 2.86 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.28 (0.34), residues: 584 helix: 1.44 (0.26), residues: 331 sheet: 0.62 (0.66), residues: 57 loop : 0.03 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.008 TRP C 133 HIS 0.007 0.002 HIS A1167 PHE 0.025 0.005 PHE A 615 TYR 0.047 0.007 TYR C 154 ARG 0.007 0.001 ARG A 975 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 182 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.7285 (mttt) cc_final: 0.6984 (mmtm) REVERT: A 1172 MET cc_start: 0.7568 (mmp) cc_final: 0.6645 (mmt) REVERT: C 75 GLN cc_start: 0.7771 (mt0) cc_final: 0.7216 (tt0) REVERT: C 160 GLU cc_start: 0.6719 (mt-10) cc_final: 0.6412 (mt-10) outliers start: 3 outliers final: 1 residues processed: 185 average time/residue: 0.2501 time to fit residues: 55.2726 Evaluate side-chains 96 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1174 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.5980 chunk 46 optimal weight: 0.2980 chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 ASN A 611 ASN A 621 GLN A 716 ASN A 746 GLN A 749 GLN C 85 GLN C 174 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5352 Z= 0.256 Angle : 0.627 6.448 7189 Z= 0.348 Chirality : 0.043 0.189 757 Planarity : 0.005 0.043 894 Dihedral : 9.284 150.525 728 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.14 % Allowed : 8.93 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 2.15 (0.34), residues: 584 helix: 2.37 (0.26), residues: 348 sheet: -0.05 (0.54), residues: 72 loop : 0.11 (0.49), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 669 HIS 0.011 0.002 HIS C 84 PHE 0.018 0.002 PHE A 651 TYR 0.024 0.002 TYR A1120 ARG 0.007 0.001 ARG C 130 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.7391 (mttt) cc_final: 0.6972 (mmtm) REVERT: A 840 PHE cc_start: 0.7591 (m-80) cc_final: 0.7126 (m-80) REVERT: A 848 MET cc_start: 0.7650 (mmm) cc_final: 0.7432 (mmt) REVERT: A 1090 LYS cc_start: 0.6703 (tppt) cc_final: 0.6051 (pttp) REVERT: A 1172 MET cc_start: 0.7774 (mmp) cc_final: 0.6889 (mmp) outliers start: 12 outliers final: 7 residues processed: 132 average time/residue: 0.2313 time to fit residues: 37.4630 Evaluate side-chains 89 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 148 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 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 714 ASN C 52 GLN C 85 GLN C 111 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5352 Z= 0.285 Angle : 0.617 10.419 7189 Z= 0.334 Chirality : 0.042 0.153 757 Planarity : 0.004 0.036 894 Dihedral : 8.177 122.760 728 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.68 % Allowed : 13.39 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.80 (0.34), residues: 584 helix: 2.14 (0.26), residues: 353 sheet: -0.62 (0.53), residues: 73 loop : 0.03 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 669 HIS 0.004 0.001 HIS C 84 PHE 0.018 0.002 PHE A 651 TYR 0.017 0.002 TYR A1120 ARG 0.004 0.001 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.7463 (mttt) cc_final: 0.7138 (mmtm) REVERT: A 840 PHE cc_start: 0.7642 (m-80) cc_final: 0.7262 (m-80) REVERT: A 848 MET cc_start: 0.7798 (mmm) cc_final: 0.7352 (mmt) REVERT: A 1090 LYS cc_start: 0.6443 (tppt) cc_final: 0.5904 (pttp) outliers start: 15 outliers final: 12 residues processed: 106 average time/residue: 0.1905 time to fit residues: 25.8520 Evaluate side-chains 88 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 148 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 58 optimal weight: 0.1980 chunk 29 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN A 756 HIS A 886 ASN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5352 Z= 0.228 Angle : 0.561 10.244 7189 Z= 0.303 Chirality : 0.040 0.162 757 Planarity : 0.004 0.034 894 Dihedral : 7.677 103.497 728 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.86 % Allowed : 13.93 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.89 (0.34), residues: 584 helix: 2.27 (0.26), residues: 353 sheet: -0.75 (0.54), residues: 73 loop : 0.00 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 978 HIS 0.004 0.001 HIS A1167 PHE 0.014 0.002 PHE A 651 TYR 0.020 0.002 TYR A 595 ARG 0.005 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.7465 (mttt) cc_final: 0.7161 (mmtm) REVERT: A 840 PHE cc_start: 0.7554 (m-80) cc_final: 0.7235 (m-80) REVERT: A 848 MET cc_start: 0.7830 (mmm) cc_final: 0.7583 (mmt) REVERT: A 1090 LYS cc_start: 0.6105 (tppt) cc_final: 0.5650 (pttt) outliers start: 16 outliers final: 8 residues processed: 106 average time/residue: 0.2025 time to fit residues: 27.6706 Evaluate side-chains 90 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 148 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 19 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5352 Z= 0.257 Angle : 0.607 10.999 7189 Z= 0.321 Chirality : 0.041 0.161 757 Planarity : 0.004 0.040 894 Dihedral : 7.445 88.540 728 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.68 % Allowed : 16.43 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.61 (0.34), residues: 584 helix: 2.04 (0.26), residues: 353 sheet: -0.94 (0.54), residues: 72 loop : -0.04 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 978 HIS 0.003 0.001 HIS A1167 PHE 0.017 0.002 PHE A 651 TYR 0.022 0.002 TYR A 595 ARG 0.006 0.001 ARG A 844 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.7416 (mttt) cc_final: 0.7109 (mmtm) REVERT: A 840 PHE cc_start: 0.7575 (m-80) cc_final: 0.7266 (m-80) REVERT: A 1090 LYS cc_start: 0.6124 (tppt) cc_final: 0.5616 (pttt) outliers start: 15 outliers final: 11 residues processed: 102 average time/residue: 0.2008 time to fit residues: 26.0458 Evaluate side-chains 95 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 148 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 14 optimal weight: 0.2980 chunk 59 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 6 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 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.5485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5352 Z= 0.224 Angle : 0.561 9.201 7189 Z= 0.302 Chirality : 0.040 0.168 757 Planarity : 0.004 0.054 894 Dihedral : 7.183 74.468 728 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.04 % Allowed : 16.07 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.71 (0.35), residues: 584 helix: 2.08 (0.26), residues: 355 sheet: -1.17 (0.55), residues: 73 loop : 0.23 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 978 HIS 0.003 0.001 HIS A1167 PHE 0.013 0.002 PHE A 651 TYR 0.020 0.002 TYR A 595 ARG 0.009 0.001 ARG A 844 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.7383 (mttt) cc_final: 0.7047 (mptt) REVERT: A 840 PHE cc_start: 0.7542 (m-80) cc_final: 0.7246 (m-80) REVERT: A 1090 LYS cc_start: 0.6288 (tppt) cc_final: 0.5746 (pttt) outliers start: 17 outliers final: 9 residues processed: 96 average time/residue: 0.2045 time to fit residues: 24.9629 Evaluate side-chains 91 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 148 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.2980 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 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 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5352 Z= 0.281 Angle : 0.603 8.825 7189 Z= 0.324 Chirality : 0.042 0.170 757 Planarity : 0.004 0.070 894 Dihedral : 7.223 64.224 728 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.14 % Allowed : 17.32 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.37 (0.35), residues: 584 helix: 1.83 (0.26), residues: 355 sheet: -1.34 (0.56), residues: 74 loop : 0.07 (0.54), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 978 HIS 0.003 0.001 HIS A 702 PHE 0.026 0.002 PHE C 123 TYR 0.019 0.002 TYR A 595 ARG 0.005 0.001 ARG A 844 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.7506 (mttt) cc_final: 0.7109 (mmtm) REVERT: A 1090 LYS cc_start: 0.6249 (tppt) cc_final: 0.5665 (pttt) outliers start: 12 outliers final: 11 residues processed: 97 average time/residue: 0.2175 time to fit residues: 26.6105 Evaluate side-chains 89 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 148 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.5727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5352 Z= 0.318 Angle : 0.616 8.421 7189 Z= 0.334 Chirality : 0.042 0.172 757 Planarity : 0.004 0.041 894 Dihedral : 7.232 57.076 728 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.14 % Allowed : 17.50 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.34), residues: 584 helix: 1.67 (0.26), residues: 353 sheet: -1.34 (0.57), residues: 73 loop : -0.34 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 669 HIS 0.003 0.001 HIS A 702 PHE 0.021 0.002 PHE C 123 TYR 0.019 0.002 TYR A 595 ARG 0.004 0.000 ARG C 130 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1090 LYS cc_start: 0.6194 (tppt) cc_final: 0.5647 (pttt) outliers start: 12 outliers final: 11 residues processed: 89 average time/residue: 0.2028 time to fit residues: 23.1069 Evaluate side-chains 92 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 148 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 60 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 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.5817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5352 Z= 0.263 Angle : 0.593 8.244 7189 Z= 0.322 Chirality : 0.041 0.172 757 Planarity : 0.004 0.062 894 Dihedral : 7.069 56.153 728 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.32 % Allowed : 17.50 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.35), residues: 584 helix: 1.74 (0.26), residues: 355 sheet: -1.42 (0.56), residues: 75 loop : -0.24 (0.53), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 669 HIS 0.003 0.001 HIS A1167 PHE 0.022 0.002 PHE C 123 TYR 0.017 0.002 TYR A 595 ARG 0.006 0.001 ARG C 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LYS cc_start: 0.7114 (mttp) cc_final: 0.6749 (mptt) REVERT: A 1090 LYS cc_start: 0.6175 (tppt) cc_final: 0.5655 (pttt) REVERT: C 175 LYS cc_start: 0.8174 (mttp) cc_final: 0.7886 (mttp) outliers start: 13 outliers final: 11 residues processed: 90 average time/residue: 0.1817 time to fit residues: 21.3534 Evaluate side-chains 88 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 148 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 5 optimal weight: 0.0670 chunk 37 optimal weight: 0.8980 chunk 29 optimal weight: 0.0980 chunk 38 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 44 optimal weight: 0.0980 chunk 7 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 overall best weight: 0.2518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 GLN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.6017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5352 Z= 0.163 Angle : 0.542 7.787 7189 Z= 0.297 Chirality : 0.039 0.162 757 Planarity : 0.004 0.061 894 Dihedral : 6.639 55.182 728 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.14 % Allowed : 17.86 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.63 (0.36), residues: 584 helix: 2.20 (0.27), residues: 355 sheet: -1.40 (0.56), residues: 74 loop : -0.17 (0.54), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 979 HIS 0.003 0.001 HIS A1167 PHE 0.022 0.002 PHE C 123 TYR 0.017 0.001 TYR A 595 ARG 0.007 0.000 ARG A 845 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1168 Ramachandran restraints generated. 584 Oldfield, 0 Emsley, 584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1090 LYS cc_start: 0.6152 (tppt) cc_final: 0.5694 (pttt) outliers start: 12 outliers final: 8 residues processed: 89 average time/residue: 0.1825 time to fit residues: 21.2853 Evaluate side-chains 85 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 TYR Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1174 CYS Chi-restraints excluded: chain C residue 148 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 49 optimal weight: 0.0980 chunk 6 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** 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 = 0.4511 r_free = 0.4511 target = 0.202002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.167569 restraints weight = 5968.163| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 2.76 r_work: 0.4011 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.6013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5352 Z= 0.243 Angle : 0.580 7.878 7189 Z= 0.315 Chirality : 0.041 0.187 757 Planarity : 0.004 0.057 894 Dihedral : 6.790 55.882 728 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.43 % Allowed : 18.21 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.41 (0.35), residues: 584 helix: 2.01 (0.26), residues: 355 sheet: -1.41 (0.56), residues: 74 loop : -0.26 (0.54), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 669 HIS 0.003 0.001 HIS A1167 PHE 0.030 0.002 PHE A 655 TYR 0.017 0.002 TYR A 595 ARG 0.007 0.001 ARG A 845 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1680.04 seconds wall clock time: 31 minutes 23.88 seconds (1883.88 seconds total)