Starting phenix.real_space_refine on Fri Dec 27 18:27:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7stf_25427/12_2024/7stf_25427.cif Found real_map, /net/cci-nas-00/data/ceres_data/7stf_25427/12_2024/7stf_25427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7stf_25427/12_2024/7stf_25427.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7stf_25427/12_2024/7stf_25427.map" model { file = "/net/cci-nas-00/data/ceres_data/7stf_25427/12_2024/7stf_25427.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7stf_25427/12_2024/7stf_25427.cif" } resolution = 3.14 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= 0.001 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: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 4030 2.51 5 N 1104 2.21 5 O 1257 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6414 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1599 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 13, 'TRANS': 202} Chain breaks: 1 Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 62 Classifications: {'peptide': 10} Modifications used: {'COO': 1} Link IDs: {'TRANS': 9} Chain: "L" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1663 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "A" Number of atoms: 2247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2247 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 13, 'TRANS': 262} Chain: "B" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 843 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 95} Time building chain proxies: 4.47, per 1000 atoms: 0.70 Number of scatterers: 6414 At special positions: 0 Unit cell: (70.052, 64.144, 145.168, 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 23 16.00 O 1257 8.00 N 1104 7.00 C 4030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 259 " distance=2.04 Simple disulfide: pdb=" SG CYS B 45 " - pdb=" SG CYS B 100 " 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 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 965.0 milliseconds 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1520 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 16 sheets defined 12.5% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'H' and resid 193 through 200 Processing helix chain 'L' and resid 124 through 129 removed outlier: 3.652A pdb=" N LYS L 128 " --> pdb=" O ASP L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 191 removed outlier: 3.861A pdb=" N TYR L 188 " --> pdb=" O SER L 184 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS L 191 " --> pdb=" O ASP L 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 55 removed outlier: 4.616A pdb=" N GLN A 54 " --> pdb=" O TRP A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 78 Processing helix chain 'A' and resid 80 through 85 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 151 through 175 Processing helix chain 'A' and resid 225 through 228 removed outlier: 3.633A pdb=" N THR A 228 " --> pdb=" O THR A 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 225 through 228' Processing helix chain 'A' and resid 252 through 255 removed outlier: 3.654A pdb=" N GLN A 255 " --> pdb=" O GLY A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing sheet with id=AA1, first strand: chain 'H' and resid 45 through 46 removed outlier: 3.567A pdb=" N GLN H 39 " --> pdb=" O VAL H 93 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 127 through 131 removed outlier: 4.749A pdb=" N LYS H 151 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU H 186 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 127 through 131 Processing sheet with id=AA4, first strand: chain 'H' and resid 159 through 162 removed outlier: 3.865A pdb=" N TYR H 202 " --> pdb=" O VAL H 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 19 through 22 removed outlier: 3.786A pdb=" N THR L 74 " --> pdb=" O SER L 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 44 through 46 Processing sheet with id=AA7, first strand: chain 'L' and resid 116 through 120 removed outlier: 3.910A pdb=" N PHE L 118 " --> pdb=" O LEU L 137 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU L 137 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE L 120 " --> pdb=" O VAL L 135 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL L 135 " --> pdb=" O PHE L 120 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 147 through 148 removed outlier: 3.755A pdb=" N THR L 199 " --> pdb=" O LYS L 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 168 through 169 Processing sheet with id=AB1, first strand: chain 'A' and resid 6 through 10 removed outlier: 6.959A pdb=" N GLY A 26 " --> pdb=" O PHE A 33 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 96 through 97 Processing sheet with id=AB3, first strand: chain 'A' and resid 186 through 192 Processing sheet with id=AB4, first strand: chain 'A' and resid 186 through 192 Processing sheet with id=AB5, first strand: chain 'A' and resid 222 through 223 removed outlier: 3.624A pdb=" N THR A 214 " --> pdb=" O GLN A 262 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.777A pdb=" N PHE B 90 " --> pdb=" O ASN B 41 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 60 through 61 removed outlier: 3.713A pdb=" N GLU B 64 " --> pdb=" O LYS B 61 " (cutoff:3.500A) 167 hydrogen bonds defined for protein. 417 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: 1.51 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2076 1.34 - 1.47: 1710 1.47 - 1.59: 2755 1.59 - 1.72: 0 1.72 - 1.85: 32 Bond restraints: 6573 Sorted by residual: bond pdb=" C ARG H 98 " pdb=" N ALA H 99 " ideal model delta sigma weight residual 1.335 1.275 0.060 1.97e-02 2.58e+03 9.41e+00 bond pdb=" CB GLN L 89 " pdb=" CG GLN L 89 " ideal model delta sigma weight residual 1.520 1.435 0.085 3.00e-02 1.11e+03 8.06e+00 bond pdb=" CA TYR L 55 " pdb=" CB TYR L 55 " ideal model delta sigma weight residual 1.534 1.488 0.045 1.72e-02 3.38e+03 6.94e+00 bond pdb=" CG ARG H 98 " pdb=" CD ARG H 98 " ideal model delta sigma weight residual 1.520 1.448 0.072 3.00e-02 1.11e+03 5.80e+00 bond pdb=" N PHE L 53 " pdb=" CA PHE L 53 " ideal model delta sigma weight residual 1.463 1.433 0.030 1.27e-02 6.20e+03 5.53e+00 ... (remaining 6568 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 8668 3.09 - 6.18: 230 6.18 - 9.26: 31 9.26 - 12.35: 4 12.35 - 15.44: 2 Bond angle restraints: 8935 Sorted by residual: angle pdb=" C PHE B 50 " pdb=" N HIS B 51 " pdb=" CA HIS B 51 " ideal model delta sigma weight residual 121.80 106.36 15.44 2.44e+00 1.68e-01 4.00e+01 angle pdb=" C SER L 52 " pdb=" N PHE L 53 " pdb=" CA PHE L 53 " ideal model delta sigma weight residual 121.72 131.19 -9.47 1.54e+00 4.22e-01 3.78e+01 angle pdb=" C GLN L 90 " pdb=" N SER L 91 " pdb=" CA SER L 91 " ideal model delta sigma weight residual 121.54 132.85 -11.31 1.91e+00 2.74e-01 3.51e+01 angle pdb=" C ILE L 48 " pdb=" N TYR L 49 " pdb=" CA TYR L 49 " ideal model delta sigma weight residual 122.42 113.90 8.52 1.55e+00 4.16e-01 3.02e+01 angle pdb=" N TYR L 92 " pdb=" CA TYR L 92 " pdb=" C TYR L 92 " ideal model delta sigma weight residual 110.80 122.19 -11.39 2.13e+00 2.20e-01 2.86e+01 ... (remaining 8930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 3403 16.18 - 32.36: 405 32.36 - 48.53: 79 48.53 - 64.71: 15 64.71 - 80.89: 15 Dihedral angle restraints: 3917 sinusoidal: 1545 harmonic: 2372 Sorted by residual: dihedral pdb=" CA SER L 91 " pdb=" C SER L 91 " pdb=" N TYR L 92 " pdb=" CA TYR L 92 " ideal model delta harmonic sigma weight residual -180.00 -124.10 -55.90 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA ASP A 29 " pdb=" C ASP A 29 " pdb=" N ASP A 30 " pdb=" CA ASP A 30 " ideal model delta harmonic sigma weight residual 180.00 134.30 45.70 0 5.00e+00 4.00e-02 8.35e+01 dihedral pdb=" CA ASN H 77 " pdb=" C ASN H 77 " pdb=" N THR H 78 " pdb=" CA THR H 78 " ideal model delta harmonic sigma weight residual -180.00 -140.14 -39.86 0 5.00e+00 4.00e-02 6.36e+01 ... (remaining 3914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 882 0.105 - 0.209: 82 0.209 - 0.314: 1 0.314 - 0.418: 1 0.418 - 0.523: 1 Chirality restraints: 967 Sorted by residual: chirality pdb=" CG LEU L 46 " pdb=" CB LEU L 46 " pdb=" CD1 LEU L 46 " pdb=" CD2 LEU L 46 " both_signs ideal model delta sigma weight residual False -2.59 -2.07 -0.52 2.00e-01 2.50e+01 6.84e+00 chirality pdb=" CG LEU L 73 " pdb=" CB LEU L 73 " pdb=" CD1 LEU L 73 " pdb=" CD2 LEU L 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA MET H 52 " pdb=" N MET H 52 " pdb=" C MET H 52 " pdb=" CB MET H 52 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 964 not shown) Planarity restraints: 1161 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 125 " -0.061 5.00e-02 4.00e+02 9.25e-02 1.37e+01 pdb=" N PRO H 126 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO H 126 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO H 126 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 160 " 0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C LEU A 160 " -0.063 2.00e-02 2.50e+03 pdb=" O LEU A 160 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP A 161 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 109 " 0.031 2.00e-02 2.50e+03 2.12e-02 8.98e+00 pdb=" CG TYR H 109 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR H 109 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR H 109 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR H 109 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR H 109 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR H 109 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR H 109 " 0.006 2.00e-02 2.50e+03 ... (remaining 1158 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 134 2.58 - 3.16: 6039 3.16 - 3.74: 10420 3.74 - 4.32: 14730 4.32 - 4.90: 23459 Nonbonded interactions: 54782 Sorted by model distance: nonbonded pdb=" NH1 ARG L 24 " pdb=" O ASP L 70 " model vdw 1.998 3.120 nonbonded pdb=" OG SER B 31 " pdb=" O HIS B 33 " model vdw 2.054 3.040 nonbonded pdb=" O HIS H 208 " pdb=" OG SER H 211 " model vdw 2.115 3.040 nonbonded pdb=" OG SER H 75 " pdb=" OD1 ASN H 77 " model vdw 2.120 3.040 nonbonded pdb=" O VAL H 2 " pdb=" ND2 ASN H 101 " model vdw 2.164 3.120 ... (remaining 54777 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: 1.650 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: 0.040 Set scattering table: 0.060 Process input model: 17.570 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 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 0.085 6573 Z= 0.599 Angle : 1.206 15.438 8935 Z= 0.665 Chirality : 0.062 0.523 967 Planarity : 0.007 0.093 1161 Dihedral : 15.262 80.889 2376 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 37.36 Ramachandran Plot: Outliers : 0.75 % Allowed : 20.12 % Favored : 79.13 % Rotamer: Outliers : 0.14 % Allowed : 0.85 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 1.04 % 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: -3.76 (0.27), residues: 805 helix: -1.22 (0.53), residues: 87 sheet: -1.69 (0.34), residues: 211 loop : -3.30 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP H 162 HIS 0.012 0.003 HIS H 57 PHE 0.044 0.004 PHE L 95 TYR 0.050 0.005 TYR H 109 ARG 0.013 0.001 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: H 35 HIS cc_start: 0.7543 (m170) cc_final: 0.7150 (m-70) REVERT: B 39 LYS cc_start: 0.7565 (mmtm) cc_final: 0.7345 (mptt) outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.2603 time to fit residues: 31.7660 Evaluate side-chains 72 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6573 Z= 0.286 Angle : 0.913 10.607 8935 Z= 0.485 Chirality : 0.051 0.201 967 Planarity : 0.006 0.059 1161 Dihedral : 8.448 69.716 896 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 22.46 Ramachandran Plot: Outliers : 0.25 % Allowed : 15.90 % Favored : 83.85 % Rotamer: Outliers : 0.85 % Allowed : 10.10 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.65 % 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: -3.59 (0.28), residues: 805 helix: -0.67 (0.55), residues: 97 sheet: -1.66 (0.33), residues: 226 loop : -3.29 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 204 HIS 0.011 0.002 HIS B 51 PHE 0.030 0.003 PHE L 95 TYR 0.024 0.002 TYR L 49 ARG 0.006 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.6730 (p0) cc_final: 0.6287 (m-30) REVERT: H 98 ARG cc_start: 0.6709 (tpp-160) cc_final: 0.6381 (mtt-85) REVERT: H 110 TRP cc_start: 0.4839 (p90) cc_final: 0.4183 (p90) REVERT: H 153 TYR cc_start: 0.6070 (p90) cc_final: 0.5436 (p90) REVERT: B 37 ASN cc_start: 0.7479 (m110) cc_final: 0.7129 (m-40) outliers start: 6 outliers final: 6 residues processed: 96 average time/residue: 0.2265 time to fit residues: 28.2259 Evaluate side-chains 76 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 40 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6573 Z= 0.299 Angle : 0.871 10.728 8935 Z= 0.461 Chirality : 0.049 0.240 967 Planarity : 0.006 0.059 1161 Dihedral : 8.082 66.155 896 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 22.54 Ramachandran Plot: Outliers : 0.25 % Allowed : 16.40 % Favored : 83.35 % Rotamer: Outliers : 2.70 % Allowed : 14.22 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.65 % 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: -3.51 (0.28), residues: 805 helix: -0.56 (0.55), residues: 96 sheet: -1.54 (0.34), residues: 215 loop : -3.27 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 204 HIS 0.009 0.001 HIS B 51 PHE 0.013 0.002 PHE H 129 TYR 0.025 0.002 TYR L 49 ARG 0.006 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.728 Fit side-chains REVERT: H 31 TYR cc_start: 0.6290 (OUTLIER) cc_final: 0.5686 (t80) REVERT: H 73 ASP cc_start: 0.6844 (p0) cc_final: 0.6451 (m-30) REVERT: H 153 TYR cc_start: 0.6281 (p90) cc_final: 0.5561 (p90) REVERT: L 55 TYR cc_start: 0.5978 (t80) cc_final: 0.5772 (t80) REVERT: B 116 ASP cc_start: 0.8080 (t0) cc_final: 0.7830 (t0) outliers start: 19 outliers final: 11 residues processed: 89 average time/residue: 0.2117 time to fit residues: 24.4844 Evaluate side-chains 78 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 40 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 163 ASN L 212 ASN A 242 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 6573 Z= 0.475 Angle : 0.959 12.218 8935 Z= 0.510 Chirality : 0.053 0.311 967 Planarity : 0.007 0.055 1161 Dihedral : 8.423 66.779 896 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 25.57 Ramachandran Plot: Outliers : 0.37 % Allowed : 17.89 % Favored : 81.74 % Rotamer: Outliers : 3.84 % Allowed : 15.65 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.65 % 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: -3.73 (0.28), residues: 805 helix: -0.85 (0.53), residues: 96 sheet: -1.74 (0.34), residues: 212 loop : -3.35 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 204 HIS 0.011 0.002 HIS B 51 PHE 0.020 0.003 PHE L 83 TYR 0.040 0.003 TYR L 49 ARG 0.005 0.001 ARG L 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.786 Fit side-chains REVERT: H 31 TYR cc_start: 0.6375 (OUTLIER) cc_final: 0.5623 (t80) REVERT: H 153 TYR cc_start: 0.6427 (p90) cc_final: 0.5620 (p90) REVERT: B 36 GLU cc_start: 0.6046 (tp30) cc_final: 0.5842 (tp30) REVERT: B 39 LYS cc_start: 0.7879 (mmtm) cc_final: 0.7625 (mmtm) REVERT: B 116 ASP cc_start: 0.8208 (t0) cc_final: 0.7933 (t0) outliers start: 27 outliers final: 18 residues processed: 96 average time/residue: 0.1961 time to fit residues: 24.9502 Evaluate side-chains 83 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 40 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 19 optimal weight: 20.0000 chunk 26 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6573 Z= 0.262 Angle : 0.831 10.506 8935 Z= 0.437 Chirality : 0.049 0.229 967 Planarity : 0.006 0.075 1161 Dihedral : 7.882 62.754 896 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.25 % Allowed : 16.02 % Favored : 83.73 % Rotamer: Outliers : 3.13 % Allowed : 17.35 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -3.59 (0.27), residues: 805 helix: -0.59 (0.54), residues: 96 sheet: -1.68 (0.35), residues: 205 loop : -3.26 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 204 HIS 0.009 0.002 HIS B 51 PHE 0.021 0.002 PHE H 107 TYR 0.021 0.002 TYR A 84 ARG 0.004 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 31 TYR cc_start: 0.6018 (OUTLIER) cc_final: 0.5720 (t80) REVERT: H 73 ASP cc_start: 0.6906 (p0) cc_final: 0.6523 (m-30) REVERT: H 105 TYR cc_start: 0.7522 (OUTLIER) cc_final: 0.5926 (t80) REVERT: H 153 TYR cc_start: 0.6353 (p90) cc_final: 0.5659 (p90) REVERT: B 116 ASP cc_start: 0.8111 (t0) cc_final: 0.7794 (t0) outliers start: 22 outliers final: 15 residues processed: 94 average time/residue: 0.2036 time to fit residues: 25.2394 Evaluate side-chains 84 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 40 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.0570 chunk 15 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 6573 Z= 0.359 Angle : 0.874 10.661 8935 Z= 0.461 Chirality : 0.050 0.276 967 Planarity : 0.006 0.071 1161 Dihedral : 7.961 62.697 896 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 23.18 Ramachandran Plot: Outliers : 0.25 % Allowed : 18.01 % Favored : 81.74 % Rotamer: Outliers : 3.13 % Allowed : 19.35 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.65 % 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: -3.73 (0.27), residues: 805 helix: -0.69 (0.52), residues: 102 sheet: -1.68 (0.35), residues: 202 loop : -3.43 (0.24), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 204 HIS 0.010 0.002 HIS B 51 PHE 0.016 0.002 PHE H 107 TYR 0.031 0.003 TYR L 49 ARG 0.007 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.743 Fit side-chains REVERT: H 31 TYR cc_start: 0.6089 (OUTLIER) cc_final: 0.5711 (t80) REVERT: H 77 ASN cc_start: 0.7088 (m110) cc_final: 0.6801 (t0) REVERT: H 98 ARG cc_start: 0.6708 (ttp-170) cc_final: 0.6310 (ttm110) REVERT: H 153 TYR cc_start: 0.6318 (p90) cc_final: 0.5568 (p90) REVERT: B 116 ASP cc_start: 0.8182 (t0) cc_final: 0.7881 (t0) outliers start: 22 outliers final: 21 residues processed: 91 average time/residue: 0.1927 time to fit residues: 23.3992 Evaluate side-chains 89 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 90 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6573 Z= 0.265 Angle : 0.838 10.334 8935 Z= 0.437 Chirality : 0.048 0.233 967 Planarity : 0.006 0.069 1161 Dihedral : 7.691 59.046 896 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.25 % Allowed : 15.53 % Favored : 84.22 % Rotamer: Outliers : 3.70 % Allowed : 19.91 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -3.59 (0.27), residues: 805 helix: -0.51 (0.53), residues: 101 sheet: -1.59 (0.35), residues: 200 loop : -3.33 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 110 HIS 0.009 0.001 HIS B 51 PHE 0.021 0.002 PHE L 120 TYR 0.027 0.002 TYR H 95 ARG 0.004 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: H 31 TYR cc_start: 0.6057 (OUTLIER) cc_final: 0.5793 (t80) REVERT: H 35 HIS cc_start: 0.7438 (m-70) cc_final: 0.7129 (m90) REVERT: H 73 ASP cc_start: 0.6961 (p0) cc_final: 0.6590 (m-30) REVERT: H 105 TYR cc_start: 0.7416 (OUTLIER) cc_final: 0.5789 (t80) REVERT: H 153 TYR cc_start: 0.6419 (p90) cc_final: 0.5673 (p90) REVERT: B 116 ASP cc_start: 0.8120 (t0) cc_final: 0.7807 (t0) outliers start: 26 outliers final: 20 residues processed: 96 average time/residue: 0.1856 time to fit residues: 23.8411 Evaluate side-chains 93 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 90 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 0.0010 chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6573 Z= 0.240 Angle : 0.813 10.019 8935 Z= 0.423 Chirality : 0.047 0.217 967 Planarity : 0.006 0.068 1161 Dihedral : 7.386 53.163 896 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.25 % Allowed : 15.90 % Favored : 83.85 % Rotamer: Outliers : 3.70 % Allowed : 20.34 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -3.48 (0.28), residues: 805 helix: -0.34 (0.54), residues: 100 sheet: -1.62 (0.34), residues: 219 loop : -3.26 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 110 HIS 0.009 0.001 HIS B 51 PHE 0.014 0.002 PHE H 107 TYR 0.024 0.002 TYR A 84 ARG 0.005 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: H 35 HIS cc_start: 0.7316 (m-70) cc_final: 0.7049 (m90) REVERT: H 73 ASP cc_start: 0.6871 (p0) cc_final: 0.6584 (m-30) REVERT: H 105 TYR cc_start: 0.7295 (OUTLIER) cc_final: 0.5471 (t80) REVERT: H 153 TYR cc_start: 0.6381 (p90) cc_final: 0.5713 (p90) REVERT: B 36 GLU cc_start: 0.5827 (tp30) cc_final: 0.5585 (tp30) REVERT: B 116 ASP cc_start: 0.8107 (t0) cc_final: 0.7774 (t0) outliers start: 26 outliers final: 19 residues processed: 97 average time/residue: 0.1961 time to fit residues: 25.6517 Evaluate side-chains 93 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 90 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 46 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: H 77 ASN ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 6573 Z= 0.232 Angle : 0.797 9.942 8935 Z= 0.414 Chirality : 0.047 0.214 967 Planarity : 0.006 0.068 1161 Dihedral : 7.266 52.263 896 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.37 % Allowed : 14.78 % Favored : 84.84 % Rotamer: Outliers : 3.56 % Allowed : 21.19 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -3.37 (0.28), residues: 805 helix: -0.28 (0.55), residues: 100 sheet: -1.48 (0.34), residues: 227 loop : -3.24 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 204 HIS 0.009 0.001 HIS B 51 PHE 0.019 0.002 PHE L 120 TYR 0.023 0.002 TYR A 84 ARG 0.007 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.638 Fit side-chains REVERT: H 31 TYR cc_start: 0.6289 (OUTLIER) cc_final: 0.5721 (t80) REVERT: H 83 MET cc_start: 0.5436 (tpt) cc_final: 0.4669 (tpp) REVERT: H 105 TYR cc_start: 0.7407 (OUTLIER) cc_final: 0.5707 (t80) REVERT: H 153 TYR cc_start: 0.6385 (p90) cc_final: 0.5630 (p90) REVERT: L 120 PHE cc_start: 0.4282 (m-80) cc_final: 0.3781 (m-80) REVERT: B 36 GLU cc_start: 0.5900 (tp30) cc_final: 0.5595 (tp30) REVERT: B 116 ASP cc_start: 0.8093 (t0) cc_final: 0.7755 (t0) outliers start: 25 outliers final: 18 residues processed: 88 average time/residue: 0.1841 time to fit residues: 21.9090 Evaluate side-chains 90 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 90 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 50 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 6573 Z= 0.358 Angle : 0.873 10.517 8935 Z= 0.457 Chirality : 0.050 0.211 967 Planarity : 0.007 0.067 1161 Dihedral : 7.737 64.121 896 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 24.05 Ramachandran Plot: Outliers : 0.37 % Allowed : 17.89 % Favored : 81.74 % Rotamer: Outliers : 3.13 % Allowed : 21.48 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -3.47 (0.28), residues: 805 helix: -0.43 (0.54), residues: 101 sheet: -1.32 (0.35), residues: 206 loop : -3.36 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 110 HIS 0.011 0.002 HIS B 51 PHE 0.018 0.002 PHE L 120 TYR 0.033 0.003 TYR L 49 ARG 0.008 0.001 ARG H 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: H 35 HIS cc_start: 0.7503 (m-70) cc_final: 0.7158 (m90) REVERT: H 83 MET cc_start: 0.5679 (tpt) cc_final: 0.4974 (tpp) REVERT: H 105 TYR cc_start: 0.7590 (OUTLIER) cc_final: 0.5862 (t80) REVERT: H 153 TYR cc_start: 0.6419 (p90) cc_final: 0.5633 (p90) REVERT: L 120 PHE cc_start: 0.4057 (m-80) cc_final: 0.3766 (m-80) REVERT: B 116 ASP cc_start: 0.8200 (t0) cc_final: 0.7867 (t0) outliers start: 22 outliers final: 18 residues processed: 90 average time/residue: 0.1847 time to fit residues: 22.5566 Evaluate side-chains 91 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 90 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.140950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.107122 restraints weight = 13340.742| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 2.95 r_work: 0.3883 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 6573 Z= 0.241 Angle : 0.811 9.900 8935 Z= 0.421 Chirality : 0.047 0.199 967 Planarity : 0.006 0.067 1161 Dihedral : 7.452 61.464 896 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.25 % Allowed : 15.03 % Favored : 84.72 % Rotamer: Outliers : 2.70 % Allowed : 22.19 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -3.39 (0.28), residues: 805 helix: -0.28 (0.55), residues: 100 sheet: -1.32 (0.35), residues: 212 loop : -3.32 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 204 HIS 0.008 0.001 HIS B 51 PHE 0.024 0.002 PHE H 107 TYR 0.020 0.002 TYR H 184 ARG 0.005 0.000 ARG L 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1790.27 seconds wall clock time: 34 minutes 8.72 seconds (2048.72 seconds total)