Starting phenix.real_space_refine on Mon Sep 23 18:13:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y97_10733/09_2024/6y97_10733.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y97_10733/09_2024/6y97_10733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y97_10733/09_2024/6y97_10733.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y97_10733/09_2024/6y97_10733.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y97_10733/09_2024/6y97_10733.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y97_10733/09_2024/6y97_10733.cif" } resolution = 4.33 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= 0.026 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 36 5.16 5 C 2840 2.51 5 N 700 2.21 5 O 790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4366 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1310 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "B" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1310 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "H" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 906 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "L" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 840 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 101} Time building chain proxies: 3.90, per 1000 atoms: 0.89 Number of scatterers: 4366 At special positions: 0 Unit cell: (61.05, 65.934, 118.03, 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 36 16.00 O 790 8.00 N 700 7.00 C 2840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 167 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 167 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " 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: 1.14 Conformation dependent library (CDL) restraints added in 488.7 milliseconds 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1032 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 4 sheets defined 47.3% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 50 through 70 removed outlier: 4.157A pdb=" N ALA A 54 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 55 " --> pdb=" O THR A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.626A pdb=" N VAL A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 100 removed outlier: 3.955A pdb=" N TRP A 89 " --> pdb=" O TRP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 143 Processing helix chain 'A' and resid 152 through 156 Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 177 through 213 removed outlier: 4.121A pdb=" N GLU A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 51 removed outlier: 3.880A pdb=" N SER B 49 " --> pdb=" O MET B 46 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LYS B 50 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR B 51 " --> pdb=" O GLU B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 71 Processing helix chain 'B' and resid 79 through 84 Processing helix chain 'B' and resid 85 through 102 removed outlier: 3.855A pdb=" N TRP B 89 " --> pdb=" O TRP B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 143 removed outlier: 4.301A pdb=" N MET B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASN B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.521A pdb=" N LYS B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASN B 176 " --> pdb=" O SER B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 213 removed outlier: 3.617A pdb=" N GLN B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.980A pdb=" N SER H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.510A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS H 22 " --> pdb=" O ALA H 79 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU H 82 " --> pdb=" O THR H 69 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR H 69 " --> pdb=" O GLU H 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.177A pdb=" N GLU H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.646A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER L 22 " --> pdb=" O THR L 7 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR L 77 " --> pdb=" O SER L 70 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER L 70 " --> pdb=" O THR L 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 58 through 59 removed outlier: 4.056A pdb=" N ASN L 58 " --> pdb=" O TYR L 54 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR L 54 " --> pdb=" O ASN L 58 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLN L 50 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU L 42 " --> pdb=" O GLN L 50 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR L 39 " --> pdb=" O ALA L 94 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN L 95 " --> pdb=" O THR L 102 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N THR L 102 " --> pdb=" O GLN L 95 " (cutoff:3.500A) 216 hydrogen bonds defined for protein. 609 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: 1.08 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1335 1.35 - 1.46: 1057 1.46 - 1.58: 2016 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 4468 Sorted by residual: bond pdb=" N GLN L 55 " pdb=" CA GLN L 55 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.78e+00 bond pdb=" CB PRO B 79 " pdb=" CG PRO B 79 " ideal model delta sigma weight residual 1.492 1.547 -0.055 5.00e-02 4.00e+02 1.23e+00 bond pdb=" CB LYS B 175 " pdb=" CG LYS B 175 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.07e+00 bond pdb=" CB LYS B 50 " pdb=" CG LYS B 50 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.07e-01 bond pdb=" CG LYS B 175 " pdb=" CD LYS B 175 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.05e-01 ... (remaining 4463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 5971 2.11 - 4.21: 72 4.21 - 6.32: 8 6.32 - 8.43: 3 8.43 - 10.53: 1 Bond angle restraints: 6055 Sorted by residual: angle pdb=" CB LYS B 175 " pdb=" CG LYS B 175 " pdb=" CD LYS B 175 " ideal model delta sigma weight residual 111.30 118.60 -7.30 2.30e+00 1.89e-01 1.01e+01 angle pdb=" C GLN L 43 " pdb=" N LYS L 44 " pdb=" CA LYS L 44 " ideal model delta sigma weight residual 121.95 111.42 10.53 3.74e+00 7.15e-02 7.93e+00 angle pdb=" CA GLN L 55 " pdb=" CB GLN L 55 " pdb=" CG GLN L 55 " ideal model delta sigma weight residual 114.10 118.84 -4.74 2.00e+00 2.50e-01 5.61e+00 angle pdb=" CA LYS B 50 " pdb=" CB LYS B 50 " pdb=" CG LYS B 50 " ideal model delta sigma weight residual 114.10 118.74 -4.64 2.00e+00 2.50e-01 5.38e+00 angle pdb=" C GLN L 55 " pdb=" N MET L 56 " pdb=" CA MET L 56 " ideal model delta sigma weight residual 121.54 125.86 -4.32 1.91e+00 2.74e-01 5.12e+00 ... (remaining 6050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 2369 17.99 - 35.98: 227 35.98 - 53.97: 46 53.97 - 71.96: 5 71.96 - 89.95: 5 Dihedral angle restraints: 2652 sinusoidal: 1031 harmonic: 1621 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 93 " pdb=" CB CYS L 93 " ideal model delta sinusoidal sigma weight residual 93.00 55.10 37.90 1 1.00e+01 1.00e-02 2.02e+01 dihedral pdb=" CB MET A 93 " pdb=" CG MET A 93 " pdb=" SD MET A 93 " pdb=" CE MET A 93 " ideal model delta sinusoidal sigma weight residual -60.00 -113.09 53.09 3 1.50e+01 4.44e-03 9.17e+00 dihedral pdb=" CB MET A 136 " pdb=" CG MET A 136 " pdb=" SD MET A 136 " pdb=" CE MET A 136 " ideal model delta sinusoidal sigma weight residual 180.00 127.86 52.14 3 1.50e+01 4.44e-03 9.09e+00 ... (remaining 2649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 461 0.034 - 0.069: 154 0.069 - 0.103: 60 0.103 - 0.137: 12 0.137 - 0.172: 1 Chirality restraints: 688 Sorted by residual: chirality pdb=" CA GLN L 55 " pdb=" N GLN L 55 " pdb=" C GLN L 55 " pdb=" CB GLN L 55 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA ILE B 143 " pdb=" N ILE B 143 " pdb=" C ILE B 143 " pdb=" CB ILE B 143 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ILE L 53 " pdb=" N ILE L 53 " pdb=" C ILE L 53 " pdb=" CB ILE L 53 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.61e-01 ... (remaining 685 not shown) Planarity restraints: 748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 78 " 0.065 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO B 79 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO B 79 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 79 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 63 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO L 64 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO L 64 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO L 64 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 94 " -0.007 2.00e-02 2.50e+03 9.89e-03 1.96e+00 pdb=" CG TYR A 94 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 94 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 94 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 94 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 94 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 94 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 94 " 0.000 2.00e-02 2.50e+03 ... (remaining 745 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 80 2.70 - 3.25: 4316 3.25 - 3.80: 6674 3.80 - 4.35: 7774 4.35 - 4.90: 13128 Nonbonded interactions: 31972 Sorted by model distance: nonbonded pdb=" OH TYR B 161 " pdb=" OG SER H 30 " model vdw 2.147 3.040 nonbonded pdb=" OH TYR A 86 " pdb=" O ALA A 126 " model vdw 2.176 3.040 nonbonded pdb=" OH TYR A 182 " pdb=" O ASN B 163 " model vdw 2.213 3.040 nonbonded pdb=" OG1 THR H 69 " pdb=" O GLU H 82 " model vdw 2.230 3.040 nonbonded pdb=" OD1 ASN A 171 " pdb=" OG SER A 173 " model vdw 2.271 3.040 ... (remaining 31967 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.330 Find NCS groups from input model: 0.090 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 4468 Z= 0.163 Angle : 0.578 10.533 6055 Z= 0.293 Chirality : 0.040 0.172 688 Planarity : 0.005 0.098 748 Dihedral : 14.610 89.950 1608 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 1.11 (0.38), residues: 556 helix: 2.81 (0.36), residues: 210 sheet: 0.41 (0.53), residues: 92 loop : -1.00 (0.43), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 109 HIS 0.003 0.001 HIS A 63 PHE 0.015 0.001 PHE B 146 TYR 0.024 0.001 TYR A 94 ARG 0.003 0.000 ARG L 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 LYS cc_start: 0.9217 (tmtt) cc_final: 0.8963 (tmmt) REVERT: B 163 ASN cc_start: 0.6919 (t0) cc_final: 0.6613 (t0) REVERT: H 46 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7361 (tm-30) REVERT: H 48 MET cc_start: 0.6951 (ppp) cc_final: 0.6250 (ppp) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1348 time to fit residues: 28.0988 Evaluate side-chains 134 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 HIS ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4468 Z= 0.254 Angle : 0.634 6.848 6055 Z= 0.327 Chirality : 0.043 0.146 688 Planarity : 0.005 0.056 748 Dihedral : 4.281 18.140 603 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.21 % Allowed : 7.07 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.90 (0.37), residues: 556 helix: 2.23 (0.34), residues: 226 sheet: 0.89 (0.53), residues: 90 loop : -1.19 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 89 HIS 0.004 0.001 HIS B 63 PHE 0.035 0.003 PHE A 62 TYR 0.028 0.002 TYR A 94 ARG 0.008 0.001 ARG H 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 154 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.8516 (pp) cc_final: 0.7932 (tt) REVERT: A 166 ASN cc_start: 0.7970 (t0) cc_final: 0.7746 (t0) REVERT: A 187 GLN cc_start: 0.8481 (mt0) cc_final: 0.8218 (mt0) REVERT: B 50 LYS cc_start: 0.9363 (tmtt) cc_final: 0.9098 (tmmt) REVERT: B 124 LEU cc_start: 0.9443 (mm) cc_final: 0.9207 (mt) REVERT: H 46 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7607 (tm-30) REVERT: H 47 TRP cc_start: 0.8810 (t60) cc_final: 0.8295 (t60) REVERT: H 48 MET cc_start: 0.7420 (ppp) cc_final: 0.7152 (ppp) REVERT: L 42 LEU cc_start: 0.8639 (mm) cc_final: 0.8332 (mm) REVERT: L 107 THR cc_start: 0.7126 (p) cc_final: 0.6897 (p) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.1297 time to fit residues: 25.9790 Evaluate side-chains 129 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 HIS ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4468 Z= 0.205 Angle : 0.612 6.445 6055 Z= 0.312 Chirality : 0.042 0.133 688 Planarity : 0.005 0.050 748 Dihedral : 4.207 18.436 603 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.21 % Allowed : 4.78 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 1.00 (0.38), residues: 556 helix: 2.54 (0.34), residues: 225 sheet: 0.72 (0.53), residues: 88 loop : -1.26 (0.43), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 89 HIS 0.002 0.001 HIS A 63 PHE 0.019 0.002 PHE A 62 TYR 0.041 0.002 TYR A 94 ARG 0.002 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.8594 (pp) cc_final: 0.8015 (tt) REVERT: A 166 ASN cc_start: 0.7856 (t0) cc_final: 0.7303 (m110) REVERT: A 183 CYS cc_start: 0.6901 (p) cc_final: 0.6602 (p) REVERT: A 187 GLN cc_start: 0.8604 (mt0) cc_final: 0.8346 (mt0) REVERT: B 71 MET cc_start: 0.5703 (ptp) cc_final: 0.5294 (ptp) REVERT: H 47 TRP cc_start: 0.8753 (t60) cc_final: 0.8298 (t60) REVERT: H 57 ASP cc_start: 0.8344 (t70) cc_final: 0.8125 (t0) REVERT: L 42 LEU cc_start: 0.8840 (mm) cc_final: 0.8533 (mm) outliers start: 1 outliers final: 1 residues processed: 154 average time/residue: 0.1503 time to fit residues: 29.6447 Evaluate side-chains 131 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 HIS ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4468 Z= 0.202 Angle : 0.603 6.442 6055 Z= 0.308 Chirality : 0.042 0.133 688 Planarity : 0.005 0.045 748 Dihedral : 4.340 17.463 603 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 1.00 (0.37), residues: 556 helix: 2.57 (0.34), residues: 225 sheet: 1.08 (0.53), residues: 83 loop : -1.40 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 33 HIS 0.002 0.001 HIS B 63 PHE 0.017 0.002 PHE A 200 TYR 0.024 0.002 TYR A 94 ARG 0.008 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.8716 (pp) cc_final: 0.8121 (tt) REVERT: A 174 GLU cc_start: 0.8771 (mp0) cc_final: 0.8403 (mp0) REVERT: A 187 GLN cc_start: 0.8577 (mt0) cc_final: 0.8340 (mt0) REVERT: B 71 MET cc_start: 0.5805 (ptp) cc_final: 0.5502 (ptp) REVERT: B 93 MET cc_start: 0.7658 (ppp) cc_final: 0.7211 (ttp) REVERT: H 27 TYR cc_start: 0.8327 (p90) cc_final: 0.7999 (p90) REVERT: H 46 GLU cc_start: 0.7881 (pp20) cc_final: 0.7581 (pp20) REVERT: H 47 TRP cc_start: 0.8703 (t60) cc_final: 0.8047 (t60) REVERT: H 48 MET cc_start: 0.7268 (ppp) cc_final: 0.6903 (ppp) REVERT: L 107 THR cc_start: 0.7360 (p) cc_final: 0.7159 (p) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1396 time to fit residues: 27.7455 Evaluate side-chains 129 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 44 optimal weight: 0.0970 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 HIS ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4468 Z= 0.224 Angle : 0.638 6.352 6055 Z= 0.325 Chirality : 0.043 0.132 688 Planarity : 0.005 0.044 748 Dihedral : 4.526 17.532 603 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.81 (0.37), residues: 556 helix: 2.47 (0.34), residues: 225 sheet: 0.61 (0.51), residues: 88 loop : -1.45 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 33 HIS 0.002 0.001 HIS L 31 PHE 0.026 0.003 PHE A 62 TYR 0.029 0.002 TYR A 94 ARG 0.006 0.001 ARG H 50 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8793 (p) cc_final: 0.8502 (t) REVERT: A 133 LEU cc_start: 0.8714 (pp) cc_final: 0.8155 (tt) REVERT: A 166 ASN cc_start: 0.7971 (t0) cc_final: 0.7541 (m-40) REVERT: A 174 GLU cc_start: 0.8905 (mp0) cc_final: 0.8518 (mp0) REVERT: A 187 GLN cc_start: 0.8516 (mt0) cc_final: 0.8193 (mt0) REVERT: A 205 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8088 (tm-30) REVERT: B 93 MET cc_start: 0.7738 (ppp) cc_final: 0.7345 (ttp) REVERT: B 174 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7467 (tp30) REVERT: H 27 TYR cc_start: 0.8271 (p90) cc_final: 0.7968 (p90) REVERT: H 46 GLU cc_start: 0.7866 (pp20) cc_final: 0.7598 (tm-30) REVERT: H 47 TRP cc_start: 0.8698 (t60) cc_final: 0.8279 (t60) REVERT: H 48 MET cc_start: 0.7275 (ppp) cc_final: 0.7003 (ppp) REVERT: L 78 LEU cc_start: 0.6935 (tt) cc_final: 0.6599 (tt) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1475 time to fit residues: 28.2198 Evaluate side-chains 130 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.0170 chunk 50 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN B 158 HIS ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4468 Z= 0.193 Angle : 0.630 7.469 6055 Z= 0.319 Chirality : 0.043 0.137 688 Planarity : 0.004 0.045 748 Dihedral : 4.499 16.473 603 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.80 (0.37), residues: 556 helix: 2.43 (0.35), residues: 225 sheet: 0.59 (0.51), residues: 88 loop : -1.41 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 89 HIS 0.009 0.002 HIS B 145 PHE 0.027 0.002 PHE B 200 TYR 0.029 0.002 TYR A 94 ARG 0.005 0.000 ARG H 50 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8782 (p) cc_final: 0.8537 (t) REVERT: A 133 LEU cc_start: 0.8723 (pp) cc_final: 0.8403 (mm) REVERT: A 166 ASN cc_start: 0.7871 (t0) cc_final: 0.7525 (m110) REVERT: A 171 ASN cc_start: 0.8874 (p0) cc_final: 0.8293 (p0) REVERT: A 174 GLU cc_start: 0.8908 (mp0) cc_final: 0.8669 (mp0) REVERT: A 187 GLN cc_start: 0.8507 (mt0) cc_final: 0.8123 (mt0) REVERT: A 205 GLU cc_start: 0.8343 (tm-30) cc_final: 0.8078 (tm-30) REVERT: B 93 MET cc_start: 0.7657 (ppp) cc_final: 0.7210 (ttp) REVERT: H 27 TYR cc_start: 0.8193 (p90) cc_final: 0.7948 (p90) REVERT: H 46 GLU cc_start: 0.7940 (pp20) cc_final: 0.7582 (pp20) REVERT: H 47 TRP cc_start: 0.8717 (t60) cc_final: 0.8124 (t60) REVERT: H 48 MET cc_start: 0.7226 (ppp) cc_final: 0.6860 (ppp) REVERT: H 102 ASP cc_start: 0.7682 (t70) cc_final: 0.7473 (t0) REVERT: L 78 LEU cc_start: 0.6946 (tt) cc_final: 0.6595 (tt) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1462 time to fit residues: 29.7041 Evaluate side-chains 139 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN B 158 HIS ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.5608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4468 Z= 0.195 Angle : 0.621 6.957 6055 Z= 0.315 Chirality : 0.043 0.144 688 Planarity : 0.004 0.048 748 Dihedral : 4.487 16.694 603 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.70 (0.37), residues: 556 helix: 2.35 (0.35), residues: 224 sheet: 0.54 (0.52), residues: 88 loop : -1.45 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 33 HIS 0.007 0.001 HIS B 145 PHE 0.028 0.002 PHE A 62 TYR 0.028 0.002 TYR A 94 ARG 0.005 0.000 ARG H 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8821 (p) cc_final: 0.8555 (t) REVERT: A 133 LEU cc_start: 0.8746 (pp) cc_final: 0.8525 (mm) REVERT: A 159 THR cc_start: 0.5283 (p) cc_final: 0.5079 (p) REVERT: A 166 ASN cc_start: 0.7814 (t0) cc_final: 0.7529 (m110) REVERT: A 171 ASN cc_start: 0.8702 (p0) cc_final: 0.8311 (p0) REVERT: A 187 GLN cc_start: 0.8498 (mt0) cc_final: 0.8116 (mt0) REVERT: A 205 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8150 (tm-30) REVERT: H 27 TYR cc_start: 0.8205 (p90) cc_final: 0.7956 (p90) REVERT: H 46 GLU cc_start: 0.7890 (pp20) cc_final: 0.7612 (pp20) REVERT: H 47 TRP cc_start: 0.8722 (t60) cc_final: 0.8144 (t60) REVERT: H 48 MET cc_start: 0.7281 (ppp) cc_final: 0.6880 (ppp) REVERT: H 102 ASP cc_start: 0.7647 (t70) cc_final: 0.7421 (t0) REVERT: L 4 MET cc_start: 0.8427 (mpp) cc_final: 0.8151 (mpp) REVERT: L 78 LEU cc_start: 0.6976 (tt) cc_final: 0.6644 (tt) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1531 time to fit residues: 31.1838 Evaluate side-chains 136 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 0.0970 chunk 4 optimal weight: 0.8980 chunk 40 optimal weight: 0.3980 chunk 47 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 21 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN B 140 ASN B 145 HIS B 158 HIS ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.5619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4468 Z= 0.184 Angle : 0.661 8.583 6055 Z= 0.329 Chirality : 0.044 0.150 688 Planarity : 0.004 0.047 748 Dihedral : 4.460 15.699 603 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.70 (0.37), residues: 556 helix: 2.37 (0.35), residues: 223 sheet: 0.58 (0.53), residues: 88 loop : -1.49 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 33 HIS 0.009 0.002 HIS B 145 PHE 0.030 0.002 PHE B 62 TYR 0.030 0.002 TYR A 94 ARG 0.004 0.001 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8788 (p) cc_final: 0.8400 (t) REVERT: A 133 LEU cc_start: 0.8826 (pp) cc_final: 0.8541 (mm) REVERT: A 166 ASN cc_start: 0.7845 (t0) cc_final: 0.7530 (m-40) REVERT: A 171 ASN cc_start: 0.8686 (p0) cc_final: 0.8260 (p0) REVERT: A 187 GLN cc_start: 0.8500 (mt0) cc_final: 0.8168 (mt0) REVERT: A 205 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8098 (tm-30) REVERT: B 189 LEU cc_start: 0.9151 (tt) cc_final: 0.8816 (tp) REVERT: H 27 TYR cc_start: 0.8171 (p90) cc_final: 0.7916 (p90) REVERT: H 46 GLU cc_start: 0.7899 (pp20) cc_final: 0.7617 (pp20) REVERT: H 47 TRP cc_start: 0.8678 (t60) cc_final: 0.8130 (t60) REVERT: H 48 MET cc_start: 0.7166 (ppp) cc_final: 0.6813 (ppp) REVERT: L 78 LEU cc_start: 0.6974 (tt) cc_final: 0.6626 (tt) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1377 time to fit residues: 28.2413 Evaluate side-chains 134 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 HIS ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.5853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4468 Z= 0.190 Angle : 0.657 8.834 6055 Z= 0.329 Chirality : 0.044 0.156 688 Planarity : 0.005 0.048 748 Dihedral : 4.556 19.392 603 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.66 (0.37), residues: 556 helix: 2.28 (0.35), residues: 223 sheet: 0.73 (0.52), residues: 93 loop : -1.57 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 33 HIS 0.002 0.001 HIS A 145 PHE 0.025 0.002 PHE B 62 TYR 0.029 0.002 TYR A 94 ARG 0.005 0.001 ARG H 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8694 (p) cc_final: 0.8450 (t) REVERT: A 166 ASN cc_start: 0.7854 (t0) cc_final: 0.7582 (m110) REVERT: A 171 ASN cc_start: 0.8767 (p0) cc_final: 0.8208 (p0) REVERT: A 174 GLU cc_start: 0.8773 (mp0) cc_final: 0.8545 (mp0) REVERT: A 187 GLN cc_start: 0.8525 (mt0) cc_final: 0.8159 (mt0) REVERT: A 205 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8112 (tm-30) REVERT: B 189 LEU cc_start: 0.9068 (tt) cc_final: 0.8806 (tp) REVERT: H 27 TYR cc_start: 0.8176 (p90) cc_final: 0.7939 (p90) REVERT: H 46 GLU cc_start: 0.7995 (pp20) cc_final: 0.7537 (pp20) REVERT: H 47 TRP cc_start: 0.8648 (t60) cc_final: 0.7981 (t60) REVERT: H 48 MET cc_start: 0.7275 (ppp) cc_final: 0.6880 (ppp) REVERT: H 68 VAL cc_start: 0.8253 (t) cc_final: 0.7152 (t) REVERT: L 78 LEU cc_start: 0.7079 (tt) cc_final: 0.6753 (tt) REVERT: L 102 THR cc_start: 0.7972 (m) cc_final: 0.7748 (m) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1323 time to fit residues: 28.2278 Evaluate side-chains 138 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.3980 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 0.0770 chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 chunk 6 optimal weight: 0.0050 chunk 11 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 overall best weight: 0.3352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN B 158 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.5732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4468 Z= 0.174 Angle : 0.669 9.263 6055 Z= 0.332 Chirality : 0.044 0.163 688 Planarity : 0.005 0.056 748 Dihedral : 4.437 16.757 603 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.68 (0.38), residues: 556 helix: 2.29 (0.35), residues: 223 sheet: 0.50 (0.52), residues: 98 loop : -1.48 (0.43), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 105 HIS 0.003 0.001 HIS B 145 PHE 0.023 0.002 PHE B 62 TYR 0.030 0.001 TYR A 94 ARG 0.003 0.000 ARG L 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8758 (p) cc_final: 0.8378 (t) REVERT: A 166 ASN cc_start: 0.7890 (t0) cc_final: 0.7579 (m110) REVERT: A 171 ASN cc_start: 0.8702 (p0) cc_final: 0.8115 (p0) REVERT: A 187 GLN cc_start: 0.8497 (mt0) cc_final: 0.8085 (mt0) REVERT: A 205 GLU cc_start: 0.8352 (tm-30) cc_final: 0.8079 (tm-30) REVERT: B 189 LEU cc_start: 0.9047 (tt) cc_final: 0.8790 (tp) REVERT: H 27 TYR cc_start: 0.8106 (p90) cc_final: 0.7885 (p90) REVERT: H 46 GLU cc_start: 0.7988 (pp20) cc_final: 0.7580 (pp20) REVERT: H 47 TRP cc_start: 0.8609 (t60) cc_final: 0.7967 (t60) REVERT: H 48 MET cc_start: 0.7285 (ppp) cc_final: 0.6900 (ppp) REVERT: H 68 VAL cc_start: 0.8143 (t) cc_final: 0.7014 (t) REVERT: L 78 LEU cc_start: 0.6980 (tt) cc_final: 0.6659 (tt) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1269 time to fit residues: 26.8190 Evaluate side-chains 137 residues out of total 481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 34 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.128778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.108360 restraints weight = 11745.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.112097 restraints weight = 7455.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.114816 restraints weight = 5121.797| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.6039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4468 Z= 0.190 Angle : 0.662 9.211 6055 Z= 0.331 Chirality : 0.044 0.165 688 Planarity : 0.005 0.051 748 Dihedral : 4.540 16.584 603 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.59 (0.37), residues: 556 helix: 2.23 (0.34), residues: 223 sheet: 0.60 (0.52), residues: 93 loop : -1.56 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 105 HIS 0.003 0.001 HIS B 145 PHE 0.015 0.002 PHE B 146 TYR 0.030 0.002 TYR A 94 ARG 0.004 0.000 ARG H 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1466.73 seconds wall clock time: 26 minutes 40.97 seconds (1600.97 seconds total)