Starting phenix.real_space_refine on Tue Feb 11 18:14:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e2j_27838/02_2025/8e2j_27838_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e2j_27838/02_2025/8e2j_27838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e2j_27838/02_2025/8e2j_27838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e2j_27838/02_2025/8e2j_27838.map" model { file = "/net/cci-nas-00/data/ceres_data/8e2j_27838/02_2025/8e2j_27838_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e2j_27838/02_2025/8e2j_27838_trim.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 10 5.16 5 C 2040 2.51 5 N 576 2.21 5 O 692 1.98 5 H 2694 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6012 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2721 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "B" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2721 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "C" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 285 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'TRANS': 56} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'UNK:plan-1': 57} Unresolved non-hydrogen planarities: 57 Chain: "D" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 285 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'TRANS': 56} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'UNK:plan-1': 57} Unresolved non-hydrogen planarities: 57 Time building chain proxies: 4.03, per 1000 atoms: 0.67 Number of scatterers: 6012 At special positions: 0 Unit cell: (121.149, 121.149, 77.9675, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 O 692 8.00 N 576 7.00 C 2040 6.00 H 2694 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 433.8 milliseconds 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 900 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 127.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 12 through 65 Processing helix chain 'A' and resid 73 through 120 Processing helix chain 'A' and resid 121 through 180 Processing helix chain 'B' and resid 13 through 65 Processing helix chain 'B' and resid 66 through 69 removed outlier: 4.560A pdb=" N MET B 69 " --> pdb=" O LEU B 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 66 through 69' Processing helix chain 'B' and resid 70 through 119 removed outlier: 5.045A pdb=" N GLU B 76 " --> pdb=" O GLU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 180 Processing helix chain 'C' and resid 52 through 107 Processing helix chain 'D' and resid 52 through 107 removed outlier: 3.544A pdb=" N UNK D 57 " --> pdb=" O UNK D 53 " (cutoff:3.500A) 403 hydrogen bonds defined for protein. 1209 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: 2.19 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 2694 1.03 - 1.22: 0 1.22 - 1.42: 1358 1.42 - 1.61: 1968 1.61 - 1.81: 20 Bond restraints: 6040 Sorted by residual: bond pdb=" CB THR B 27 " pdb=" CG2 THR B 27 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.90e-01 bond pdb=" C LEU A 98 " pdb=" O LEU A 98 " ideal model delta sigma weight residual 1.237 1.225 0.011 1.17e-02 7.31e+03 9.50e-01 bond pdb=" C GLU B 140 " pdb=" O GLU B 140 " ideal model delta sigma weight residual 1.236 1.224 0.012 1.29e-02 6.01e+03 8.13e-01 bond pdb=" CB VAL B 26 " pdb=" CG2 VAL B 26 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.88e-01 bond pdb=" C VAL B 26 " pdb=" N THR B 27 " ideal model delta sigma weight residual 1.335 1.323 0.012 1.36e-02 5.41e+03 7.80e-01 ... (remaining 6035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 9978 1.15 - 2.29: 645 2.29 - 3.44: 19 3.44 - 4.59: 5 4.59 - 5.73: 1 Bond angle restraints: 10648 Sorted by residual: angle pdb=" CA TYR A 95 " pdb=" CB TYR A 95 " pdb=" CG TYR A 95 " ideal model delta sigma weight residual 113.90 119.63 -5.73 1.80e+00 3.09e-01 1.01e+01 angle pdb=" C UNK C 91 " pdb=" N UNK C 92 " pdb=" CA UNK C 92 " ideal model delta sigma weight residual 121.70 125.93 -4.23 1.80e+00 3.09e-01 5.53e+00 angle pdb=" N GLU A 183 " pdb=" CA GLU A 183 " pdb=" C GLU A 183 " ideal model delta sigma weight residual 110.80 115.19 -4.39 2.13e+00 2.20e-01 4.24e+00 angle pdb=" C HIS A 131 " pdb=" N ILE A 132 " pdb=" CA ILE A 132 " ideal model delta sigma weight residual 120.60 122.99 -2.39 1.29e+00 6.01e-01 3.43e+00 angle pdb=" C ALA B 44 " pdb=" N ILE B 45 " pdb=" CA ILE B 45 " ideal model delta sigma weight residual 120.53 123.05 -2.52 1.41e+00 5.03e-01 3.18e+00 ... (remaining 10643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 2675 17.77 - 35.54: 152 35.54 - 53.31: 44 53.31 - 71.08: 12 71.08 - 88.85: 9 Dihedral angle restraints: 2892 sinusoidal: 1404 harmonic: 1488 Sorted by residual: dihedral pdb=" CA GLU A 72 " pdb=" C GLU A 72 " pdb=" N GLU A 73 " pdb=" CA GLU A 73 " ideal model delta harmonic sigma weight residual 180.00 162.32 17.68 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA LEU A 66 " pdb=" C LEU A 66 " pdb=" N GLY A 67 " pdb=" CA GLY A 67 " ideal model delta harmonic sigma weight residual -180.00 -162.76 -17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA UNK C 51 " pdb=" C UNK C 51 " pdb=" N UNK C 52 " pdb=" CA UNK C 52 " ideal model delta harmonic sigma weight residual -180.00 -163.77 -16.23 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 2889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 420 0.030 - 0.061: 119 0.061 - 0.091: 12 0.091 - 0.121: 2 0.121 - 0.151: 1 Chirality restraints: 554 Sorted by residual: chirality pdb=" CA TYR A 95 " pdb=" N TYR A 95 " pdb=" C TYR A 95 " pdb=" CB TYR A 95 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.73e-01 chirality pdb=" CA ILE A 132 " pdb=" N ILE A 132 " pdb=" C ILE A 132 " pdb=" CB ILE A 132 " both_signs ideal model delta sigma weight residual False 2.43 2.53 -0.10 2.00e-01 2.50e+01 2.51e-01 chirality pdb=" CA GLU A 183 " pdb=" N GLU A 183 " pdb=" C GLU A 183 " pdb=" CB GLU A 183 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 2.19e-01 ... (remaining 551 not shown) Planarity restraints: 936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 78 " 0.013 2.00e-02 2.50e+03 1.83e-02 1.34e+01 pdb=" CG TRP B 78 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TRP B 78 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP B 78 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B 78 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TRP B 78 " 0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP B 78 " -0.029 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 78 " 0.020 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 78 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP B 78 " 0.034 2.00e-02 2.50e+03 pdb=" HD1 TRP B 78 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 TRP B 78 " 0.018 2.00e-02 2.50e+03 pdb=" HE3 TRP B 78 " -0.000 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 78 " -0.019 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 78 " 0.012 2.00e-02 2.50e+03 pdb=" HH2 TRP B 78 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 165 " -0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C THR B 165 " 0.061 2.00e-02 2.50e+03 pdb=" O THR B 165 " -0.023 2.00e-02 2.50e+03 pdb=" N GLN B 166 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " -0.007 2.00e-02 2.50e+03 2.02e-02 1.22e+01 pdb=" CG TYR B 59 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " 0.041 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " 0.028 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " -0.027 2.00e-02 2.50e+03 pdb=" HD1 TYR B 59 " -0.020 2.00e-02 2.50e+03 pdb=" HD2 TYR B 59 " -0.010 2.00e-02 2.50e+03 pdb=" HE1 TYR B 59 " -0.014 2.00e-02 2.50e+03 pdb=" HE2 TYR B 59 " -0.020 2.00e-02 2.50e+03 ... (remaining 933 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 140 2.09 - 2.72: 9530 2.72 - 3.34: 17591 3.34 - 3.97: 20508 3.97 - 4.60: 33116 Nonbonded interactions: 80885 Sorted by model distance: nonbonded pdb=" O ARG A 21 " pdb=" HG SER A 24 " model vdw 1.462 2.450 nonbonded pdb=" O GLN B 61 " pdb=" HG SER B 64 " model vdw 1.559 2.450 nonbonded pdb=" O ARG B 21 " pdb=" HG SER B 24 " model vdw 1.606 2.450 nonbonded pdb="HH11 ARG B 129 " pdb=" OD1 ASN B 130 " model vdw 1.611 2.450 nonbonded pdb=" O GLN A 61 " pdb=" HG SER A 64 " model vdw 1.611 2.450 ... (remaining 80880 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 1.840 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: 0.130 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.420 Find NCS groups from input model: 0.120 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: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 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 : 0.003 0.033 3346 Z= 0.207 Angle : 0.629 5.734 4544 Z= 0.386 Chirality : 0.028 0.151 554 Planarity : 0.008 0.084 592 Dihedral : 15.861 88.851 1154 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.70 % Allowed : 6.08 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.37), residues: 342 helix: 0.02 (0.24), residues: 315 sheet: None (None), residues: 0 loop : -1.70 (1.15), residues: 27 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.010 TRP B 78 HIS 0.010 0.003 HIS A 131 PHE 0.017 0.009 PHE B 33 TYR 0.043 0.007 TYR A 95 ARG 0.018 0.002 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8291 (ttp) cc_final: 0.8078 (tmm) REVERT: A 145 LEU cc_start: 0.8834 (mp) cc_final: 0.8594 (tp) REVERT: B 33 PHE cc_start: 0.8349 (t80) cc_final: 0.8108 (t80) outliers start: 8 outliers final: 5 residues processed: 124 average time/residue: 0.5200 time to fit residues: 71.7975 Evaluate side-chains 97 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 98 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 34 optimal weight: 20.0000 chunk 13 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 39 optimal weight: 30.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.119486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.095666 restraints weight = 33169.885| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 3.75 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3346 Z= 0.287 Angle : 0.538 4.877 4544 Z= 0.312 Chirality : 0.027 0.107 554 Planarity : 0.003 0.030 592 Dihedral : 6.369 55.339 503 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Rotamer: Outliers : 2.36 % Allowed : 13.18 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.42), residues: 342 helix: 1.76 (0.26), residues: 320 sheet: None (None), residues: 0 loop : -1.05 (1.60), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 78 HIS 0.004 0.002 HIS A 131 PHE 0.013 0.004 PHE A 33 TYR 0.023 0.002 TYR A 95 ARG 0.005 0.001 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 ILE cc_start: 0.8818 (mt) cc_final: 0.8596 (mt) outliers start: 7 outliers final: 7 residues processed: 96 average time/residue: 0.5186 time to fit residues: 56.3766 Evaluate side-chains 91 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 98 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 5 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 23 optimal weight: 0.0270 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.8442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS B 131 HIS B 133 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.121587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.097592 restraints weight = 33753.357| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 3.82 r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3346 Z= 0.188 Angle : 0.429 4.768 4544 Z= 0.251 Chirality : 0.025 0.092 554 Planarity : 0.003 0.025 592 Dihedral : 6.406 55.605 503 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 3.38 % Allowed : 14.86 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.43 (0.42), residues: 342 helix: 2.48 (0.26), residues: 322 sheet: None (None), residues: 0 loop : -1.64 (1.47), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 78 HIS 0.005 0.001 HIS B 131 PHE 0.005 0.002 PHE B 33 TYR 0.019 0.002 TYR A 95 ARG 0.004 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 ILE cc_start: 0.8702 (mt) cc_final: 0.8482 (mt) outliers start: 10 outliers final: 9 residues processed: 90 average time/residue: 0.5382 time to fit residues: 54.3586 Evaluate side-chains 89 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 144 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 30 optimal weight: 0.4980 chunk 34 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS B 131 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.121974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.098340 restraints weight = 34378.887| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 3.83 r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3346 Z= 0.198 Angle : 0.444 4.864 4544 Z= 0.259 Chirality : 0.026 0.102 554 Planarity : 0.002 0.022 592 Dihedral : 6.385 57.015 503 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Rotamer: Outliers : 2.70 % Allowed : 16.55 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.53 (0.41), residues: 342 helix: 2.58 (0.26), residues: 323 sheet: None (None), residues: 0 loop : -2.61 (1.09), residues: 19 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 78 HIS 0.004 0.001 HIS B 131 PHE 0.021 0.004 PHE A 33 TYR 0.020 0.001 TYR A 95 ARG 0.002 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 ILE cc_start: 0.8752 (mt) cc_final: 0.8532 (mt) outliers start: 8 outliers final: 8 residues processed: 84 average time/residue: 0.4756 time to fit residues: 45.1716 Evaluate side-chains 87 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 144 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 31 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 1 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.121234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.097558 restraints weight = 34076.845| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 3.78 r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3346 Z= 0.211 Angle : 0.444 4.872 4544 Z= 0.260 Chirality : 0.025 0.093 554 Planarity : 0.002 0.030 592 Dihedral : 5.915 59.375 499 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 2.70 % Allowed : 15.88 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.78 (0.41), residues: 342 helix: 2.72 (0.26), residues: 321 sheet: None (None), residues: 0 loop : -1.70 (1.35), residues: 21 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 78 HIS 0.010 0.002 HIS B 131 PHE 0.014 0.004 PHE A 33 TYR 0.020 0.002 TYR A 95 ARG 0.003 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 ILE cc_start: 0.8707 (mt) cc_final: 0.8496 (mt) REVERT: B 95 TYR cc_start: 0.6901 (OUTLIER) cc_final: 0.5811 (t80) REVERT: B 131 HIS cc_start: 0.6431 (t-170) cc_final: 0.6227 (t-170) outliers start: 8 outliers final: 6 residues processed: 85 average time/residue: 0.4706 time to fit residues: 45.3527 Evaluate side-chains 86 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 144 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 2 optimal weight: 0.7980 chunk 34 optimal weight: 20.0000 chunk 14 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.121327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.097658 restraints weight = 33818.410| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 3.80 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.5695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3346 Z= 0.224 Angle : 0.454 5.158 4544 Z= 0.266 Chirality : 0.026 0.093 554 Planarity : 0.002 0.023 592 Dihedral : 5.873 56.634 499 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 3.04 % Allowed : 16.89 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.94 (0.41), residues: 342 helix: 2.83 (0.25), residues: 321 sheet: None (None), residues: 0 loop : -1.65 (1.35), residues: 21 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 78 HIS 0.006 0.001 HIS B 131 PHE 0.013 0.003 PHE A 33 TYR 0.020 0.001 TYR A 95 ARG 0.003 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 ILE cc_start: 0.8694 (mt) cc_final: 0.8475 (mt) REVERT: B 95 TYR cc_start: 0.6957 (OUTLIER) cc_final: 0.5764 (t80) outliers start: 9 outliers final: 7 residues processed: 87 average time/residue: 0.5162 time to fit residues: 50.2903 Evaluate side-chains 87 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 144 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 7 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.0570 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.121092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.097165 restraints weight = 34330.393| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 3.85 r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3346 Z= 0.216 Angle : 0.460 5.336 4544 Z= 0.264 Chirality : 0.025 0.100 554 Planarity : 0.002 0.022 592 Dihedral : 5.851 55.317 499 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.70 % Allowed : 17.91 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.11 (0.41), residues: 342 helix: 2.94 (0.25), residues: 321 sheet: None (None), residues: 0 loop : -1.60 (1.35), residues: 21 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 78 HIS 0.004 0.001 HIS B 131 PHE 0.013 0.003 PHE A 33 TYR 0.019 0.001 TYR A 95 ARG 0.001 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 ILE cc_start: 0.8735 (mt) cc_final: 0.8521 (mt) REVERT: B 95 TYR cc_start: 0.7041 (OUTLIER) cc_final: 0.5770 (t80) outliers start: 8 outliers final: 7 residues processed: 85 average time/residue: 0.5022 time to fit residues: 47.9619 Evaluate side-chains 88 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.116572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.092679 restraints weight = 35272.643| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 3.64 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.6229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 3346 Z= 0.461 Angle : 0.718 5.717 4544 Z= 0.412 Chirality : 0.032 0.120 554 Planarity : 0.004 0.024 592 Dihedral : 5.493 53.174 497 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.72 % Allowed : 18.24 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.42), residues: 342 helix: 1.81 (0.26), residues: 321 sheet: None (None), residues: 0 loop : -1.84 (1.22), residues: 21 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 102 HIS 0.004 0.002 HIS B 92 PHE 0.028 0.007 PHE A 33 TYR 0.026 0.002 TYR A 95 ARG 0.004 0.001 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 TYR cc_start: 0.8039 (m-80) cc_final: 0.7715 (m-10) REVERT: B 81 ILE cc_start: 0.8831 (mt) cc_final: 0.8618 (mt) outliers start: 11 outliers final: 11 residues processed: 88 average time/residue: 0.4778 time to fit residues: 47.5262 Evaluate side-chains 89 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 144 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 0 optimal weight: 2.9990 chunk 39 optimal weight: 30.0000 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.119370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.095261 restraints weight = 33564.094| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 3.72 r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.6300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3346 Z= 0.242 Angle : 0.519 6.041 4544 Z= 0.296 Chirality : 0.026 0.102 554 Planarity : 0.003 0.021 592 Dihedral : 5.544 58.160 497 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.36 % Allowed : 19.59 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.35 (0.42), residues: 342 helix: 2.42 (0.26), residues: 322 sheet: None (None), residues: 0 loop : -1.49 (1.42), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 78 HIS 0.004 0.001 HIS B 131 PHE 0.013 0.003 PHE A 33 TYR 0.027 0.002 TYR B 53 ARG 0.002 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 TYR cc_start: 0.8016 (m-80) cc_final: 0.7691 (m-10) REVERT: B 81 ILE cc_start: 0.8808 (mt) cc_final: 0.8601 (mt) REVERT: B 95 TYR cc_start: 0.6931 (OUTLIER) cc_final: 0.5843 (t80) outliers start: 7 outliers final: 6 residues processed: 88 average time/residue: 0.5035 time to fit residues: 49.7078 Evaluate side-chains 91 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 144 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 8 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.0980 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 133 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.122024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.097999 restraints weight = 33846.978| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 3.81 r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.6466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3346 Z= 0.180 Angle : 0.459 6.149 4544 Z= 0.263 Chirality : 0.025 0.096 554 Planarity : 0.002 0.024 592 Dihedral : 5.518 58.516 497 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.03 % Allowed : 19.93 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.96 (0.41), residues: 342 helix: 2.84 (0.25), residues: 323 sheet: None (None), residues: 0 loop : -2.23 (1.16), residues: 19 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 102 HIS 0.005 0.001 HIS B 131 PHE 0.006 0.002 PHE A 33 TYR 0.017 0.002 TYR A 95 ARG 0.002 0.000 ARG B 85 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.7537 (p0) cc_final: 0.6895 (t70) REVERT: A 59 TYR cc_start: 0.7976 (m-80) cc_final: 0.7599 (m-10) REVERT: A 95 TYR cc_start: 0.7707 (OUTLIER) cc_final: 0.6736 (t80) REVERT: A 102 TRP cc_start: 0.5874 (t60) cc_final: 0.5263 (t60) REVERT: B 95 TYR cc_start: 0.6657 (OUTLIER) cc_final: 0.4902 (t80) outliers start: 6 outliers final: 4 residues processed: 85 average time/residue: 0.4972 time to fit residues: 47.5538 Evaluate side-chains 87 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 144 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.0060 chunk 11 optimal weight: 0.6980 chunk 40 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 HIS ** 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 = 0.4558 r_free = 0.4558 target = 0.121839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.098067 restraints weight = 34201.334| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 3.81 r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.6615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3346 Z= 0.187 Angle : 0.487 5.663 4544 Z= 0.279 Chirality : 0.025 0.117 554 Planarity : 0.003 0.033 592 Dihedral : 5.528 57.661 497 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.03 % Allowed : 20.95 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.10 (0.41), residues: 342 helix: 2.92 (0.25), residues: 320 sheet: None (None), residues: 0 loop : -1.12 (1.36), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 102 HIS 0.015 0.002 HIS B 131 PHE 0.005 0.001 PHE A 33 TYR 0.017 0.002 TYR A 95 ARG 0.005 0.000 ARG B 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3388.84 seconds wall clock time: 60 minutes 17.55 seconds (3617.55 seconds total)