Starting phenix.real_space_refine on Tue Feb 11 08:46:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bf8_16016/02_2025/8bf8_16016.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bf8_16016/02_2025/8bf8_16016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bf8_16016/02_2025/8bf8_16016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bf8_16016/02_2025/8bf8_16016.map" model { file = "/net/cci-nas-00/data/ceres_data/8bf8_16016/02_2025/8bf8_16016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bf8_16016/02_2025/8bf8_16016.cif" } resolution = 2.8 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 111 5.49 5 S 1 5.16 5 C 2525 2.51 5 N 871 2.21 5 O 1178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4686 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2303 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 7, 'TRANS': 294} Chain breaks: 4 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 112 Chain: "B" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 2383 Classifications: {'RNA': 111} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 5, 'rna3p_pur': 51, 'rna3p_pyr': 43} Link IDs: {'rna2p': 16, 'rna3p': 94} Chain breaks: 2 Time building chain proxies: 3.87, per 1000 atoms: 0.83 Number of scatterers: 4686 At special positions: 0 Unit cell: (84.032, 87.36, 84.864, 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 1 16.00 P 111 15.00 O 1178 8.00 N 871 7.00 C 2525 6.00 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: 1.43 Conformation dependent library (CDL) restraints added in 315.0 milliseconds 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 566 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 2 sheets defined 53.6% alpha, 16.2% beta 42 base pairs and 59 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 14 through 43 removed outlier: 3.645A pdb=" N ILE A 21 " --> pdb=" O GLN A 17 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE A 35 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR A 43 " --> pdb=" O ARG A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 65 Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 75 through 94 removed outlier: 3.766A pdb=" N LEU A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 232 Processing helix chain 'A' and resid 236 through 272 Processing helix chain 'A' and resid 299 through 315 Processing helix chain 'A' and resid 360 through 377 Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 121 removed outlier: 4.057A pdb=" N LYS A 153 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU A 172 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL A 157 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N SER A 170 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL A 159 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLU A 168 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG A 161 " --> pdb=" O HIS A 166 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N HIS A 166 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR A 167 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 171 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 10 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS A 143 " --> pdb=" O TYR A 12 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 201 153 hydrogen bonds defined for protein. 441 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 103 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 59 stacking parallelities Total time for adding SS restraints: 2.04 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 872 1.33 - 1.45: 1746 1.45 - 1.57: 2169 1.57 - 1.68: 219 1.68 - 1.80: 1 Bond restraints: 5007 Sorted by residual: bond pdb=" O3' C B -63 " pdb=" P C B -62 " ideal model delta sigma weight residual 1.607 1.587 0.020 1.50e-02 4.44e+03 1.82e+00 bond pdb=" C GLY A 189 " pdb=" O GLY A 189 " ideal model delta sigma weight residual 1.243 1.233 0.010 9.30e-03 1.16e+04 1.15e+00 bond pdb=" CB TRP A 313 " pdb=" CG TRP A 313 " ideal model delta sigma weight residual 1.498 1.470 0.028 3.10e-02 1.04e+03 8.25e-01 bond pdb=" CA ILE A 177 " pdb=" CB ILE A 177 " ideal model delta sigma weight residual 1.526 1.540 -0.014 1.55e-02 4.16e+03 8.01e-01 bond pdb=" CB PRO A 178 " pdb=" CG PRO A 178 " ideal model delta sigma weight residual 1.492 1.535 -0.043 5.00e-02 4.00e+02 7.39e-01 ... (remaining 5002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 7116 1.20 - 2.40: 153 2.40 - 3.60: 34 3.60 - 4.80: 7 4.80 - 5.99: 2 Bond angle restraints: 7312 Sorted by residual: angle pdb=" CA TYR A 309 " pdb=" CB TYR A 309 " pdb=" CG TYR A 309 " ideal model delta sigma weight residual 113.90 119.89 -5.99 1.80e+00 3.09e-01 1.11e+01 angle pdb=" O4' A B -88 " pdb=" C1' A B -88 " pdb=" N9 A B -88 " ideal model delta sigma weight residual 108.20 112.12 -3.92 1.50e+00 4.44e-01 6.83e+00 angle pdb=" C2' G B -78 " pdb=" C1' G B -78 " pdb=" N9 G B -78 " ideal model delta sigma weight residual 112.00 114.91 -2.91 1.50e+00 4.44e-01 3.75e+00 angle pdb=" C THR A 123 " pdb=" N ASN A 124 " pdb=" CA ASN A 124 " ideal model delta sigma weight residual 122.46 124.93 -2.47 1.41e+00 5.03e-01 3.07e+00 angle pdb=" C2' A B -88 " pdb=" C1' A B -88 " pdb=" N9 A B -88 " ideal model delta sigma weight residual 114.00 116.60 -2.60 1.50e+00 4.44e-01 3.00e+00 ... (remaining 7307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 2593 17.34 - 34.68: 225 34.68 - 52.02: 138 52.02 - 69.36: 155 69.36 - 86.70: 29 Dihedral angle restraints: 3140 sinusoidal: 2265 harmonic: 875 Sorted by residual: dihedral pdb=" O4' U B -89 " pdb=" C1' U B -89 " pdb=" N1 U B -89 " pdb=" C2 U B -89 " ideal model delta sinusoidal sigma weight residual -160.00 -84.08 -75.92 1 1.50e+01 4.44e-03 3.23e+01 dihedral pdb=" CB LYS A 233 " pdb=" CG LYS A 233 " pdb=" CD LYS A 233 " pdb=" CE LYS A 233 " ideal model delta sinusoidal sigma weight residual 60.00 117.41 -57.41 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" O5' C B -67 " pdb=" C5' C B -67 " pdb=" C4' C B -67 " pdb=" C3' C B -67 " ideal model delta sinusoidal sigma weight residual 55.00 -1.26 56.26 3 1.50e+01 4.44e-03 9.39e+00 ... (remaining 3137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 796 0.043 - 0.086: 89 0.086 - 0.129: 26 0.129 - 0.171: 0 0.171 - 0.214: 1 Chirality restraints: 912 Sorted by residual: chirality pdb=" C1' A B -88 " pdb=" O4' A B -88 " pdb=" C2' A B -88 " pdb=" N9 A B -88 " both_signs ideal model delta sigma weight residual False 2.44 2.22 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA TYR A 309 " pdb=" N TYR A 309 " pdb=" C TYR A 309 " pdb=" CB TYR A 309 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA ILE A 275 " pdb=" N ILE A 275 " pdb=" C ILE A 275 " pdb=" CB ILE A 275 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 ... (remaining 909 not shown) Planarity restraints: 514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B -88 " -0.028 2.00e-02 2.50e+03 1.38e-02 5.27e+00 pdb=" N9 A B -88 " 0.035 2.00e-02 2.50e+03 pdb=" C8 A B -88 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A B -88 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A B -88 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A B -88 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A B -88 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A B -88 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A B -88 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A B -88 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A B -88 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B -78 " 0.026 2.00e-02 2.50e+03 1.08e-02 3.47e+00 pdb=" N9 G B -78 " -0.025 2.00e-02 2.50e+03 pdb=" C8 G B -78 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G B -78 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B -78 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G B -78 " 0.003 2.00e-02 2.50e+03 pdb=" O6 G B -78 " 0.007 2.00e-02 2.50e+03 pdb=" N1 G B -78 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G B -78 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G B -78 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G B -78 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G B -78 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 309 " -0.015 2.00e-02 2.50e+03 1.18e-02 2.76e+00 pdb=" CG TYR A 309 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR A 309 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 309 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 309 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 309 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 309 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 309 " -0.000 2.00e-02 2.50e+03 ... (remaining 511 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 516 2.74 - 3.28: 4367 3.28 - 3.82: 9269 3.82 - 4.36: 10882 4.36 - 4.90: 15807 Nonbonded interactions: 40841 Sorted by model distance: nonbonded pdb=" O LEU A 261 " pdb=" OG1 THR A 265 " model vdw 2.203 3.040 nonbonded pdb=" NH2 ARG A 238 " pdb=" O6 G B -33 " model vdw 2.243 3.120 nonbonded pdb=" O2' A B -66 " pdb=" O2 C B -63 " model vdw 2.252 3.040 nonbonded pdb=" O2 C B-107 " pdb=" N2 G B -6 " model vdw 2.284 3.120 nonbonded pdb=" O LYS A 263 " pdb=" OG SER A 267 " model vdw 2.307 3.040 ... (remaining 40836 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.960 Find NCS groups from input model: 0.050 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:13.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 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 0.043 5007 Z= 0.178 Angle : 0.474 5.995 7312 Z= 0.248 Chirality : 0.031 0.214 912 Planarity : 0.003 0.022 514 Dihedral : 21.432 86.703 2574 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.93 % Allowed : 6.98 % Favored : 92.09 % 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: 0.92 (0.51), residues: 292 helix: 2.03 (0.40), residues: 151 sheet: -1.01 (0.85), residues: 44 loop : -0.84 (0.67), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 313 HIS 0.005 0.002 HIS A 262 PHE 0.009 0.001 PHE A 35 TYR 0.029 0.002 TYR A 309 ARG 0.002 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.262 Fit side-chains REVERT: A 168 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7675 (mt-10) REVERT: A 214 TYR cc_start: 0.8208 (m-80) cc_final: 0.7977 (m-80) outliers start: 2 outliers final: 1 residues processed: 35 average time/residue: 1.2560 time to fit residues: 45.7662 Evaluate side-chains 26 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 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 14 ASN A 64 GLN ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 ASN A 147 GLN A 156 ASN A 227 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.205303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.161398 restraints weight = 5078.232| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 1.31 r_work: 0.3744 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5007 Z= 0.247 Angle : 0.542 6.419 7312 Z= 0.279 Chirality : 0.035 0.201 912 Planarity : 0.004 0.021 514 Dihedral : 22.249 86.633 2071 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.86 % Allowed : 13.49 % Favored : 84.65 % 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: 0.83 (0.50), residues: 292 helix: 2.00 (0.40), residues: 152 sheet: -2.34 (1.40), residues: 16 loop : -0.90 (0.58), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 70 HIS 0.004 0.002 HIS A 163 PHE 0.010 0.001 PHE A 35 TYR 0.030 0.002 TYR A 309 ARG 0.003 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.346 Fit side-chains REVERT: A 147 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.6888 (tm130) REVERT: A 168 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7688 (mt-10) REVERT: A 174 GLU cc_start: 0.6680 (mt-10) cc_final: 0.6472 (mt-10) REVERT: A 214 TYR cc_start: 0.8217 (m-80) cc_final: 0.7877 (m-80) REVERT: A 223 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6127 (mmp-170) outliers start: 4 outliers final: 2 residues processed: 31 average time/residue: 1.4632 time to fit residues: 47.7679 Evaluate side-chains 29 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.204763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.160274 restraints weight = 5137.453| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.33 r_work: 0.3733 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5007 Z= 0.248 Angle : 0.535 6.461 7312 Z= 0.276 Chirality : 0.034 0.199 912 Planarity : 0.004 0.021 514 Dihedral : 22.186 84.496 2070 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.26 % Allowed : 14.42 % Favored : 82.33 % 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: 0.62 (0.49), residues: 292 helix: 1.95 (0.40), residues: 152 sheet: -1.47 (1.05), residues: 24 loop : -1.30 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 70 HIS 0.004 0.002 HIS A 163 PHE 0.006 0.001 PHE A 197 TYR 0.029 0.002 TYR A 309 ARG 0.002 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.279 Fit side-chains REVERT: A 147 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.6711 (tm130) REVERT: A 168 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7580 (mt-10) REVERT: A 223 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.6171 (mmp-170) REVERT: A 309 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.7497 (p90) outliers start: 7 outliers final: 2 residues processed: 32 average time/residue: 1.1353 time to fit residues: 38.0565 Evaluate side-chains 30 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.201757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.156765 restraints weight = 5176.705| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.39 r_work: 0.3695 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 5007 Z= 0.345 Angle : 0.605 7.190 7312 Z= 0.309 Chirality : 0.037 0.195 912 Planarity : 0.004 0.029 514 Dihedral : 22.219 84.670 2070 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.19 % Allowed : 13.95 % Favored : 81.86 % 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: 0.30 (0.48), residues: 292 helix: 1.68 (0.39), residues: 152 sheet: -1.63 (1.02), residues: 24 loop : -1.43 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 313 HIS 0.004 0.002 HIS A 163 PHE 0.008 0.002 PHE A 197 TYR 0.033 0.002 TYR A 309 ARG 0.003 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 23 time to evaluate : 0.353 Fit side-chains REVERT: A 147 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.6745 (tm130) REVERT: A 168 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7735 (mt-10) REVERT: A 223 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6229 (mmp-170) REVERT: A 309 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.7611 (p90) outliers start: 9 outliers final: 4 residues processed: 29 average time/residue: 1.2461 time to fit residues: 37.7937 Evaluate side-chains 30 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.207177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.163057 restraints weight = 5194.047| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 1.34 r_work: 0.3764 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5007 Z= 0.180 Angle : 0.505 6.233 7312 Z= 0.261 Chirality : 0.033 0.212 912 Planarity : 0.003 0.021 514 Dihedral : 22.119 82.468 2070 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.79 % Allowed : 16.74 % Favored : 80.47 % 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: 0.69 (0.49), residues: 292 helix: 2.14 (0.39), residues: 152 sheet: -1.66 (1.01), residues: 24 loop : -1.42 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 70 HIS 0.004 0.002 HIS A 163 PHE 0.005 0.001 PHE A 30 TYR 0.026 0.001 TYR A 309 ARG 0.002 0.000 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.299 Fit side-chains REVERT: A 168 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7502 (mt-10) REVERT: A 223 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6118 (mmp-170) REVERT: A 309 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.7307 (p90) outliers start: 6 outliers final: 0 residues processed: 31 average time/residue: 1.2209 time to fit residues: 39.4988 Evaluate side-chains 25 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 28 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.204243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.159775 restraints weight = 5093.191| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.38 r_work: 0.3727 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5007 Z= 0.270 Angle : 0.550 6.871 7312 Z= 0.283 Chirality : 0.035 0.197 912 Planarity : 0.004 0.021 514 Dihedral : 22.106 82.574 2070 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.72 % Allowed : 18.14 % Favored : 78.14 % 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: 0.53 (0.49), residues: 292 helix: 1.95 (0.39), residues: 152 sheet: -1.47 (1.05), residues: 24 loop : -1.47 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 313 HIS 0.004 0.002 HIS A 163 PHE 0.006 0.001 PHE A 197 TYR 0.031 0.002 TYR A 309 ARG 0.002 0.000 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.318 Fit side-chains REVERT: A 110 ARG cc_start: 0.6181 (OUTLIER) cc_final: 0.5775 (mtt180) REVERT: A 168 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7676 (mt-10) REVERT: A 223 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6128 (mmp-170) REVERT: A 309 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.7499 (p90) outliers start: 8 outliers final: 3 residues processed: 28 average time/residue: 1.4804 time to fit residues: 43.0193 Evaluate side-chains 30 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 0.3980 chunk 8 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.201082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.156422 restraints weight = 5077.117| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.41 r_work: 0.3695 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 5007 Z= 0.353 Angle : 0.612 7.192 7312 Z= 0.314 Chirality : 0.037 0.194 912 Planarity : 0.004 0.029 514 Dihedral : 22.200 83.230 2070 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.19 % Allowed : 17.67 % Favored : 78.14 % 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: 0.26 (0.48), residues: 292 helix: 1.66 (0.39), residues: 152 sheet: -1.50 (1.03), residues: 24 loop : -1.53 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 313 HIS 0.004 0.002 HIS A 163 PHE 0.009 0.002 PHE A 197 TYR 0.033 0.002 TYR A 309 ARG 0.002 0.000 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.327 Fit side-chains REVERT: A 168 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7717 (mt-10) REVERT: A 223 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.6259 (mmp-170) REVERT: A 309 TYR cc_start: 0.8214 (OUTLIER) cc_final: 0.7667 (p90) outliers start: 9 outliers final: 5 residues processed: 32 average time/residue: 1.2430 time to fit residues: 41.5209 Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 4 optimal weight: 0.0770 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.203350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.158664 restraints weight = 5122.432| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.37 r_work: 0.3717 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5007 Z= 0.272 Angle : 0.561 6.813 7312 Z= 0.291 Chirality : 0.035 0.203 912 Planarity : 0.004 0.021 514 Dihedral : 22.131 82.849 2070 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.26 % Allowed : 19.53 % Favored : 77.21 % 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: 0.40 (0.48), residues: 292 helix: 1.86 (0.39), residues: 152 sheet: -1.60 (1.01), residues: 24 loop : -1.54 (0.55), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 300 HIS 0.004 0.002 HIS A 163 PHE 0.006 0.001 PHE A 197 TYR 0.031 0.002 TYR A 309 ARG 0.003 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.341 Fit side-chains REVERT: A 168 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7667 (mt-10) REVERT: A 223 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6142 (mmp-170) REVERT: A 309 TYR cc_start: 0.8148 (OUTLIER) cc_final: 0.7534 (p90) outliers start: 7 outliers final: 4 residues processed: 28 average time/residue: 1.1961 time to fit residues: 35.1094 Evaluate side-chains 30 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 26 optimal weight: 0.0980 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.0770 chunk 33 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.210186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.166454 restraints weight = 5174.699| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 1.36 r_work: 0.3789 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5007 Z= 0.166 Angle : 0.491 6.086 7312 Z= 0.256 Chirality : 0.032 0.222 912 Planarity : 0.003 0.020 514 Dihedral : 21.959 81.401 2070 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.79 % Allowed : 19.53 % Favored : 77.67 % 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: 0.83 (0.49), residues: 292 helix: 2.41 (0.39), residues: 152 sheet: -1.48 (1.04), residues: 24 loop : -1.63 (0.55), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 70 HIS 0.004 0.002 HIS A 163 PHE 0.007 0.001 PHE A 30 TYR 0.025 0.001 TYR A 309 ARG 0.002 0.000 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.366 Fit side-chains REVERT: A 168 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7603 (mt-10) REVERT: A 213 LYS cc_start: 0.8270 (mtmm) cc_final: 0.7954 (mtmm) REVERT: A 223 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6142 (mmp-170) REVERT: A 309 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.6441 (p90) outliers start: 6 outliers final: 3 residues processed: 29 average time/residue: 1.3343 time to fit residues: 40.6699 Evaluate side-chains 30 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 chunk 18 optimal weight: 0.0060 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.210127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.166648 restraints weight = 5098.398| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 1.35 r_work: 0.3779 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5007 Z= 0.170 Angle : 0.496 6.122 7312 Z= 0.256 Chirality : 0.032 0.205 912 Planarity : 0.003 0.020 514 Dihedral : 21.903 80.326 2070 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.33 % Allowed : 20.47 % Favored : 77.21 % 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: 0.94 (0.49), residues: 292 helix: 2.54 (0.39), residues: 152 sheet: -1.40 (1.03), residues: 24 loop : -1.66 (0.55), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 70 HIS 0.004 0.002 HIS A 163 PHE 0.005 0.001 PHE A 30 TYR 0.027 0.001 TYR A 309 ARG 0.002 0.000 ARG A 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 584 Ramachandran restraints generated. 292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.378 Fit side-chains REVERT: A 168 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7587 (mt-10) REVERT: A 174 GLU cc_start: 0.6640 (mp0) cc_final: 0.6027 (mp0) REVERT: A 213 LYS cc_start: 0.8268 (mtmm) cc_final: 0.7948 (mtmm) REVERT: A 223 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6136 (mmp-170) REVERT: A 309 TYR cc_start: 0.8028 (OUTLIER) cc_final: 0.7291 (p90) outliers start: 5 outliers final: 2 residues processed: 30 average time/residue: 1.4777 time to fit residues: 46.5881 Evaluate side-chains 29 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 0.0870 chunk 29 optimal weight: 9.9990 chunk 24 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.212245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.168381 restraints weight = 5144.082| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 1.37 r_work: 0.3806 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3671 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5007 Z= 0.162 Angle : 0.483 5.876 7312 Z= 0.249 Chirality : 0.032 0.204 912 Planarity : 0.003 0.019 514 Dihedral : 21.830 78.434 2070 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.33 % Allowed : 20.00 % Favored : 77.67 % 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: 1.15 (0.50), residues: 292 helix: 2.60 (0.39), residues: 152 sheet: -0.86 (0.86), residues: 39 loop : -1.54 (0.61), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 70 HIS 0.004 0.002 HIS A 163 PHE 0.005 0.001 PHE A 30 TYR 0.025 0.001 TYR A 309 ARG 0.002 0.000 ARG A 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3797.83 seconds wall clock time: 67 minutes 44.71 seconds (4064.71 seconds total)