Starting phenix.real_space_refine on Thu Mar 6 06:25:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j6f_36003/03_2025/8j6f_36003.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j6f_36003/03_2025/8j6f_36003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j6f_36003/03_2025/8j6f_36003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j6f_36003/03_2025/8j6f_36003.map" model { file = "/net/cci-nas-00/data/ceres_data/8j6f_36003/03_2025/8j6f_36003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j6f_36003/03_2025/8j6f_36003.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1592 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 2443 2.51 5 N 657 2.21 5 O 758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3870 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1590 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1615 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 197} Chain: "I" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 571 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 5, 'TRANS': 60} Chain breaks: 3 Chain: "B" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 80 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 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: 4.18, per 1000 atoms: 1.08 Number of scatterers: 3870 At special positions: 0 Unit cell: (54.12, 64.78, 107.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 758 8.00 N 657 7.00 C 2443 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 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 I 401 " - " ASN I 221 " Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 482.7 milliseconds 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 934 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 12 sheets defined 1.8% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'H' and resid 73 through 76 Processing helix chain 'H' and resid 191 through 195 removed outlier: 3.625A pdb=" N SER H 194 " --> pdb=" O PRO H 191 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU H 195 " --> pdb=" O SER H 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 191 through 195' Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 59 removed outlier: 4.322A pdb=" N TRP H 37 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TYR H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N TRP H 35 " --> pdb=" O TYR H 51 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA H 92 " --> pdb=" O VAL H 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 126 through 130 removed outlier: 6.174A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 126 through 130 removed outlier: 6.174A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 159 through 160 removed outlier: 4.639A pdb=" N TYR H 200 " --> pdb=" O VAL H 217 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 7 removed outlier: 4.163A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.382A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.620A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 114 through 115 removed outlier: 3.732A pdb=" N CYS L 134 " --> pdb=" O SER L 177 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 144 through 148 removed outlier: 4.265A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 220 through 223 removed outlier: 5.556A pdb=" N ASN I 221 " --> pdb=" O GLN I 239 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLN I 239 " --> pdb=" O ASN I 221 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR I 237 " --> pdb=" O THR I 223 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 268 through 269 removed outlier: 3.623A pdb=" N GLU I 254 " --> pdb=" O ARG I 293 " (cutoff:3.500A) 108 hydrogen bonds defined for protein. 270 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: 1.03 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1065 1.33 - 1.45: 757 1.45 - 1.57: 2127 1.57 - 1.69: 1 1.69 - 1.81: 16 Bond restraints: 3966 Sorted by residual: bond pdb=" C ALA H 101 " pdb=" N ARG H 102 " ideal model delta sigma weight residual 1.332 1.297 0.036 1.40e-02 5.10e+03 6.49e+00 bond pdb=" CG LEU L 94 " pdb=" CD2 LEU L 94 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.27e+00 bond pdb=" SD MET H 106 " pdb=" CE MET H 106 " ideal model delta sigma weight residual 1.791 1.742 0.049 2.50e-02 1.60e+03 3.92e+00 bond pdb=" CG GLN L 90 " pdb=" CD GLN L 90 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.58e+00 bond pdb=" CA THR H 157 " pdb=" CB THR H 157 " ideal model delta sigma weight residual 1.539 1.630 -0.090 4.88e-02 4.20e+02 3.43e+00 ... (remaining 3961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 5051 1.92 - 3.83: 286 3.83 - 5.75: 42 5.75 - 7.66: 14 7.66 - 9.58: 9 Bond angle restraints: 5402 Sorted by residual: angle pdb=" C TYR L 50 " pdb=" N THR L 51 " pdb=" CA THR L 51 " ideal model delta sigma weight residual 121.54 129.30 -7.76 1.91e+00 2.74e-01 1.65e+01 angle pdb=" CB LYS H 215 " pdb=" CG LYS H 215 " pdb=" CD LYS H 215 " ideal model delta sigma weight residual 111.30 119.08 -7.78 2.30e+00 1.89e-01 1.14e+01 angle pdb=" C TRP L 148 " pdb=" N LYS L 149 " pdb=" CA LYS L 149 " ideal model delta sigma weight residual 121.54 127.86 -6.32 1.91e+00 2.74e-01 1.10e+01 angle pdb=" N PHE H 152 " pdb=" CA PHE H 152 " pdb=" C PHE H 152 " ideal model delta sigma weight residual 109.81 117.10 -7.29 2.21e+00 2.05e-01 1.09e+01 angle pdb=" N GLU H 154 " pdb=" CA GLU H 154 " pdb=" C GLU H 154 " ideal model delta sigma weight residual 108.97 114.84 -5.87 1.82e+00 3.02e-01 1.04e+01 ... (remaining 5397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 2128 17.44 - 34.88: 203 34.88 - 52.32: 40 52.32 - 69.76: 5 69.76 - 87.19: 4 Dihedral angle restraints: 2380 sinusoidal: 935 harmonic: 1445 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 148.64 -55.64 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CA GLU I 296 " pdb=" C GLU I 296 " pdb=" N GLU I 297 " pdb=" CA GLU I 297 " ideal model delta harmonic sigma weight residual 180.00 -151.29 -28.71 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA PRO H 155 " pdb=" C PRO H 155 " pdb=" N VAL H 156 " pdb=" CA VAL H 156 " ideal model delta harmonic sigma weight residual -180.00 -154.76 -25.24 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 2377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 373 0.045 - 0.090: 155 0.090 - 0.135: 60 0.135 - 0.180: 17 0.180 - 0.225: 6 Chirality restraints: 611 Sorted by residual: chirality pdb=" CA PHE H 152 " pdb=" N PHE H 152 " pdb=" C PHE H 152 " pdb=" CB PHE H 152 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB VAL B 111 " pdb=" CA VAL B 111 " pdb=" CG1 VAL B 111 " pdb=" CG2 VAL B 111 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CG LEU H 20 " pdb=" CB LEU H 20 " pdb=" CD1 LEU H 20 " pdb=" CD2 LEU H 20 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 608 not shown) Planarity restraints: 684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN H 61 " -0.083 5.00e-02 4.00e+02 1.25e-01 2.49e+01 pdb=" N PRO H 62 " 0.216 5.00e-02 4.00e+02 pdb=" CA PRO H 62 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO H 62 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN L 79 " 0.075 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO L 80 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 154 " -0.061 5.00e-02 4.00e+02 9.22e-02 1.36e+01 pdb=" N PRO H 155 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO H 155 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO H 155 " -0.051 5.00e-02 4.00e+02 ... (remaining 681 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 458 2.75 - 3.29: 3545 3.29 - 3.82: 6540 3.82 - 4.36: 7591 4.36 - 4.90: 13565 Nonbonded interactions: 31699 Sorted by model distance: nonbonded pdb=" OG SER H 36 " pdb=" OG SER H 99 " model vdw 2.208 3.040 nonbonded pdb=" OH TYR L 96 " pdb=" O PHE I 298 " model vdw 2.230 3.040 nonbonded pdb=" O ASP H 90 " pdb=" OH TYR H 94 " model vdw 2.265 3.040 nonbonded pdb=" O PRO H 173 " pdb=" OG SER L 162 " model vdw 2.273 3.040 nonbonded pdb=" O ILE L 106 " pdb=" NE2 GLN L 166 " model vdw 2.309 3.120 ... (remaining 31694 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=0.00 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: 4.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.860 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 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 : 0.009 0.099 3966 Z= 0.562 Angle : 1.060 9.576 5402 Z= 0.550 Chirality : 0.060 0.225 611 Planarity : 0.011 0.125 683 Dihedral : 14.303 87.194 1434 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -3.18 (0.37), residues: 480 helix: -5.48 (0.27), residues: 6 sheet: -2.43 (0.34), residues: 204 loop : -1.69 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP I 238 HIS 0.010 0.002 HIS I 275 PHE 0.054 0.005 PHE I 298 TYR 0.036 0.004 TYR I 249 ARG 0.011 0.001 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.421 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.2093 time to fit residues: 14.8682 Evaluate side-chains 46 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.6980 chunk 36 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.0980 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 275 HIS I 295 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.188519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.154630 restraints weight = 4006.108| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.27 r_work: 0.3720 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 3966 Z= 0.280 Angle : 0.707 11.804 5402 Z= 0.359 Chirality : 0.045 0.154 611 Planarity : 0.008 0.077 683 Dihedral : 6.218 24.818 552 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.68 % Allowed : 9.57 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -2.98 (0.38), residues: 480 helix: -5.47 (0.28), residues: 6 sheet: -2.30 (0.33), residues: 224 loop : -1.42 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 306 HIS 0.004 0.001 HIS L 55 PHE 0.012 0.002 PHE L 139 TYR 0.016 0.002 TYR I 249 ARG 0.002 0.000 ARG I 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.415 Fit side-chains REVERT: L 24 ARG cc_start: 0.6451 (mtp180) cc_final: 0.6167 (mtp-110) outliers start: 3 outliers final: 1 residues processed: 55 average time/residue: 0.1688 time to fit residues: 11.9153 Evaluate side-chains 50 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 96 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 46 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 0.0980 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 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 = 0.4223 r_free = 0.4223 target = 0.187157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.153112 restraints weight = 4005.193| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.28 r_work: 0.3701 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 3966 Z= 0.298 Angle : 0.694 8.795 5402 Z= 0.349 Chirality : 0.045 0.150 611 Planarity : 0.007 0.065 683 Dihedral : 5.924 24.969 552 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 0.91 % Allowed : 12.30 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -2.75 (0.38), residues: 480 helix: -5.44 (0.28), residues: 6 sheet: -2.09 (0.34), residues: 209 loop : -1.41 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP I 306 HIS 0.004 0.001 HIS L 55 PHE 0.014 0.002 PHE L 139 TYR 0.016 0.002 TYR I 249 ARG 0.010 0.001 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.414 Fit side-chains REVERT: L 24 ARG cc_start: 0.6529 (mtp180) cc_final: 0.6247 (mtp-110) outliers start: 4 outliers final: 3 residues processed: 55 average time/residue: 0.1971 time to fit residues: 13.5673 Evaluate side-chains 51 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain L residue 132 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 GLN ** L 199 GLN ** 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 = 0.4208 r_free = 0.4208 target = 0.185537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.151520 restraints weight = 4004.806| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.28 r_work: 0.3683 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 3966 Z= 0.322 Angle : 0.678 6.922 5402 Z= 0.343 Chirality : 0.045 0.149 611 Planarity : 0.007 0.060 683 Dihedral : 5.828 26.263 552 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 1.37 % Allowed : 14.58 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -2.74 (0.38), residues: 480 helix: -5.42 (0.29), residues: 6 sheet: -2.13 (0.35), residues: 212 loop : -1.34 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 35 HIS 0.003 0.001 HIS L 55 PHE 0.035 0.003 PHE I 298 TYR 0.017 0.002 TYR L 87 ARG 0.006 0.001 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.445 Fit side-chains REVERT: L 24 ARG cc_start: 0.6543 (mtp180) cc_final: 0.6248 (mtp-110) outliers start: 6 outliers final: 5 residues processed: 50 average time/residue: 0.1454 time to fit residues: 9.4730 Evaluate side-chains 49 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 203 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 28 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 24 optimal weight: 0.2980 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 0.0030 chunk 42 optimal weight: 0.0070 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.2808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.190261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.156680 restraints weight = 4053.506| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.28 r_work: 0.3750 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3966 Z= 0.191 Angle : 0.622 9.265 5402 Z= 0.310 Chirality : 0.044 0.149 611 Planarity : 0.006 0.056 683 Dihedral : 5.355 23.522 552 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.05 % Allowed : 15.95 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.39), residues: 480 helix: -5.39 (0.29), residues: 6 sheet: -1.88 (0.35), residues: 212 loop : -1.12 (0.41), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 35 HIS 0.002 0.000 HIS L 55 PHE 0.024 0.002 PHE I 298 TYR 0.019 0.001 TYR L 87 ARG 0.004 0.000 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.411 Fit side-chains REVERT: L 24 ARG cc_start: 0.6513 (mtp180) cc_final: 0.6227 (mtp-110) outliers start: 9 outliers final: 5 residues processed: 53 average time/residue: 0.1650 time to fit residues: 11.0810 Evaluate side-chains 49 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain I residue 289 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.0040 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 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 = 0.4223 r_free = 0.4223 target = 0.187147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.153167 restraints weight = 3997.565| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.28 r_work: 0.3705 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 3966 Z= 0.308 Angle : 0.661 9.241 5402 Z= 0.330 Chirality : 0.045 0.181 611 Planarity : 0.006 0.056 683 Dihedral : 5.408 24.150 552 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 1.37 % Allowed : 18.00 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -2.33 (0.40), residues: 480 helix: -5.42 (0.28), residues: 6 sheet: -1.84 (0.36), residues: 211 loop : -1.06 (0.41), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 35 HIS 0.003 0.001 HIS L 55 PHE 0.029 0.002 PHE I 298 TYR 0.014 0.002 TYR L 36 ARG 0.003 0.000 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.465 Fit side-chains REVERT: L 24 ARG cc_start: 0.6515 (mtp180) cc_final: 0.6214 (mtp-110) REVERT: I 306 TRP cc_start: 0.7477 (m-90) cc_final: 0.7139 (m-90) outliers start: 6 outliers final: 6 residues processed: 50 average time/residue: 0.1916 time to fit residues: 11.8526 Evaluate side-chains 50 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain I residue 289 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 0.0370 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 0.0470 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 12 optimal weight: 0.2980 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 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 = 0.4240 r_free = 0.4240 target = 0.188947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.155863 restraints weight = 3942.966| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.22 r_work: 0.3750 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 3966 Z= 0.223 Angle : 0.618 8.668 5402 Z= 0.310 Chirality : 0.043 0.170 611 Planarity : 0.006 0.055 683 Dihedral : 5.187 23.592 552 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 1.82 % Allowed : 18.00 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 (0.40), residues: 480 helix: -5.41 (0.29), residues: 6 sheet: -1.69 (0.36), residues: 213 loop : -0.96 (0.42), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 35 HIS 0.002 0.000 HIS L 55 PHE 0.028 0.002 PHE I 298 TYR 0.012 0.001 TYR I 249 ARG 0.004 0.000 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.396 Fit side-chains REVERT: L 24 ARG cc_start: 0.6490 (mtp180) cc_final: 0.6166 (mtp-110) REVERT: L 61 ARG cc_start: 0.8388 (ptt-90) cc_final: 0.8042 (ptt-90) REVERT: I 306 TRP cc_start: 0.7319 (m-90) cc_final: 0.6896 (m-90) outliers start: 8 outliers final: 7 residues processed: 50 average time/residue: 0.1717 time to fit residues: 10.7708 Evaluate side-chains 53 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain B residue 111 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 34 optimal weight: 0.0040 chunk 4 optimal weight: 0.0570 chunk 12 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 overall best weight: 0.3910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 295 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 = 0.4250 r_free = 0.4250 target = 0.190183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.156555 restraints weight = 3974.582| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.26 r_work: 0.3736 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 3966 Z= 0.237 Angle : 0.628 8.511 5402 Z= 0.313 Chirality : 0.044 0.165 611 Planarity : 0.006 0.055 683 Dihedral : 5.138 24.854 552 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 1.82 % Allowed : 18.22 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -2.05 (0.41), residues: 480 helix: -5.43 (0.28), residues: 6 sheet: -1.63 (0.37), residues: 206 loop : -0.91 (0.42), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 35 HIS 0.002 0.000 HIS L 55 PHE 0.030 0.002 PHE I 298 TYR 0.014 0.002 TYR L 36 ARG 0.004 0.000 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.467 Fit side-chains REVERT: L 24 ARG cc_start: 0.6517 (mtp180) cc_final: 0.6168 (mtp-110) REVERT: I 306 TRP cc_start: 0.7279 (m-90) cc_final: 0.6932 (m-90) outliers start: 8 outliers final: 7 residues processed: 49 average time/residue: 0.2505 time to fit residues: 15.4329 Evaluate side-chains 50 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain B residue 111 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 295 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 = 0.4203 r_free = 0.4203 target = 0.184819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.150568 restraints weight = 4023.309| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.28 r_work: 0.3673 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 3966 Z= 0.369 Angle : 0.694 7.625 5402 Z= 0.349 Chirality : 0.045 0.166 611 Planarity : 0.006 0.055 683 Dihedral : 5.507 26.014 552 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 2.73 % Allowed : 18.00 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -2.23 (0.41), residues: 480 helix: -5.45 (0.28), residues: 6 sheet: -1.80 (0.37), residues: 206 loop : -1.00 (0.42), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 35 HIS 0.003 0.001 HIS L 55 PHE 0.033 0.003 PHE I 298 TYR 0.018 0.002 TYR L 36 ARG 0.008 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.340 Fit side-chains REVERT: L 24 ARG cc_start: 0.6524 (mtp180) cc_final: 0.6146 (mtp-110) REVERT: I 297 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.5828 (pm20) outliers start: 12 outliers final: 9 residues processed: 53 average time/residue: 0.3420 time to fit residues: 22.8766 Evaluate side-chains 48 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 297 GLU Chi-restraints excluded: chain B residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 37 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 24 optimal weight: 0.0980 chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 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 = 0.4216 r_free = 0.4216 target = 0.186508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.152568 restraints weight = 4012.518| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.29 r_work: 0.3705 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 3966 Z= 0.279 Angle : 0.665 7.848 5402 Z= 0.333 Chirality : 0.045 0.164 611 Planarity : 0.006 0.055 683 Dihedral : 5.355 26.929 552 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 2.28 % Allowed : 18.91 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -2.12 (0.41), residues: 480 helix: -5.43 (0.29), residues: 6 sheet: -1.74 (0.37), residues: 206 loop : -0.90 (0.42), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP I 306 HIS 0.002 0.001 HIS L 55 PHE 0.029 0.003 PHE I 298 TYR 0.016 0.002 TYR L 36 ARG 0.008 0.001 ARG H 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.700 Fit side-chains REVERT: L 24 ARG cc_start: 0.6510 (mtp180) cc_final: 0.6122 (mtp-110) REVERT: I 250 ARG cc_start: 0.6628 (ttm110) cc_final: 0.6347 (ttm-80) outliers start: 10 outliers final: 9 residues processed: 47 average time/residue: 0.2013 time to fit residues: 12.3900 Evaluate side-chains 48 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 203 SER Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain B residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 0.0770 chunk 29 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 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 = 0.4205 r_free = 0.4205 target = 0.185227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.151310 restraints weight = 3950.503| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.27 r_work: 0.3686 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 3966 Z= 0.343 Angle : 0.695 7.215 5402 Z= 0.350 Chirality : 0.046 0.164 611 Planarity : 0.007 0.055 683 Dihedral : 5.494 27.516 552 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 2.28 % Allowed : 19.13 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -2.18 (0.41), residues: 480 helix: -5.44 (0.29), residues: 6 sheet: -1.74 (0.38), residues: 203 loop : -1.00 (0.42), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP I 306 HIS 0.003 0.001 HIS L 55 PHE 0.030 0.003 PHE I 298 TYR 0.025 0.002 TYR L 87 ARG 0.009 0.001 ARG I 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2590.29 seconds wall clock time: 47 minutes 17.87 seconds (2837.87 seconds total)