Starting phenix.real_space_refine on Mon Sep 23 18:32:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iei_35382/09_2024/8iei_35382.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iei_35382/09_2024/8iei_35382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iei_35382/09_2024/8iei_35382.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iei_35382/09_2024/8iei_35382.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iei_35382/09_2024/8iei_35382.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iei_35382/09_2024/8iei_35382.cif" } resolution = 2.62 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= 0.011 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 2 5.49 5 S 35 5.16 5 C 2961 2.51 5 N 704 2.21 5 O 767 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4469 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2135 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2230 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain breaks: 1 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 4.48, per 1000 atoms: 1.00 Number of scatterers: 4469 At special positions: 0 Unit cell: (68.04, 89.1, 102.87, 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 35 16.00 P 2 15.00 O 767 8.00 N 704 7.00 C 2961 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 216 " 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: 1.11 Conformation dependent library (CDL) restraints added in 498.1 milliseconds 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1048 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 1 sheets defined 78.3% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 46 through 74 Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 84 through 105 removed outlier: 3.560A pdb=" N ILE A 89 " --> pdb=" O PRO A 85 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A 90 " --> pdb=" O ASN A 86 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 150 Proline residue: A 137 - end of helix Processing helix chain 'A' and resid 161 through 187 removed outlier: 3.782A pdb=" N LEU A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 246 removed outlier: 4.099A pdb=" N TRP A 224 " --> pdb=" O TYR A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 281 removed outlier: 3.558A pdb=" N ASN A 265 " --> pdb=" O MET A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 327 Proline residue: A 310 - end of helix Processing helix chain 'B' and resid 46 through 74 Processing helix chain 'B' and resid 77 through 83 removed outlier: 3.692A pdb=" N SER B 83 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 105 removed outlier: 3.664A pdb=" N VAL B 90 " --> pdb=" O ASN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 149 Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 169 through 187 Processing helix chain 'B' and resid 220 through 246 removed outlier: 3.597A pdb=" N TRP B 224 " --> pdb=" O TYR B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 281 Processing helix chain 'B' and resid 284 through 332 Proline residue: B 310 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 216 removed outlier: 3.508A pdb=" N PHE A 215 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 195 " --> pdb=" O MET B 199 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 215 " --> pdb=" O LEU B 192 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1140 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: 1.28 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 645 1.31 - 1.44: 1215 1.44 - 1.56: 2638 1.56 - 1.69: 12 1.69 - 1.81: 50 Bond restraints: 4560 Sorted by residual: bond pdb=" C39 PC1 B 601 " pdb=" C3A PC1 B 601 " ideal model delta sigma weight residual 1.524 1.324 0.200 2.00e-02 2.50e+03 9.99e+01 bond pdb=" C39 PC1 A 601 " pdb=" C3A PC1 A 601 " ideal model delta sigma weight residual 1.524 1.327 0.197 2.00e-02 2.50e+03 9.74e+01 bond pdb=" C31 PC1 A 601 " pdb=" O31 PC1 A 601 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C31 PC1 B 601 " pdb=" O31 PC1 B 601 " ideal model delta sigma weight residual 1.330 1.424 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C21 PC1 B 601 " pdb=" O21 PC1 B 601 " ideal model delta sigma weight residual 1.331 1.383 -0.052 2.00e-02 2.50e+03 6.74e+00 ... (remaining 4555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 6109 2.82 - 5.63: 64 5.63 - 8.45: 14 8.45 - 11.26: 0 11.26 - 14.08: 2 Bond angle restraints: 6189 Sorted by residual: angle pdb=" O12 PC1 B 601 " pdb=" P PC1 B 601 " pdb=" O14 PC1 B 601 " ideal model delta sigma weight residual 123.67 109.59 14.08 3.00e+00 1.11e-01 2.20e+01 angle pdb=" O12 PC1 A 601 " pdb=" P PC1 A 601 " pdb=" O14 PC1 A 601 " ideal model delta sigma weight residual 123.67 109.95 13.72 3.00e+00 1.11e-01 2.09e+01 angle pdb=" CB TRP B 229 " pdb=" CG TRP B 229 " pdb=" CD2 TRP B 229 " ideal model delta sigma weight residual 126.80 131.57 -4.77 1.40e+00 5.10e-01 1.16e+01 angle pdb=" CB TRP B 229 " pdb=" CG TRP B 229 " pdb=" CD1 TRP B 229 " ideal model delta sigma weight residual 126.90 122.30 4.60 1.50e+00 4.44e-01 9.41e+00 angle pdb=" C32 PC1 A 601 " pdb=" C31 PC1 A 601 " pdb=" O31 PC1 A 601 " ideal model delta sigma weight residual 111.44 119.80 -8.36 3.00e+00 1.11e-01 7.76e+00 ... (remaining 6184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 2452 17.56 - 35.12: 196 35.12 - 52.68: 42 52.68 - 70.25: 7 70.25 - 87.81: 5 Dihedral angle restraints: 2702 sinusoidal: 1080 harmonic: 1622 Sorted by residual: dihedral pdb=" CA ILE B 228 " pdb=" C ILE B 228 " pdb=" N TRP B 229 " pdb=" CA TRP B 229 " ideal model delta harmonic sigma weight residual 180.00 159.87 20.13 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA ILE A 307 " pdb=" C ILE A 307 " pdb=" N PHE A 308 " pdb=" CA PHE A 308 " ideal model delta harmonic sigma weight residual -180.00 -160.00 -20.00 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ILE B 307 " pdb=" C ILE B 307 " pdb=" N PHE B 308 " pdb=" CA PHE B 308 " ideal model delta harmonic sigma weight residual -180.00 -161.73 -18.27 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 2699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 560 0.040 - 0.080: 152 0.080 - 0.119: 46 0.119 - 0.159: 3 0.159 - 0.199: 1 Chirality restraints: 762 Sorted by residual: chirality pdb=" CA TRP B 229 " pdb=" N TRP B 229 " pdb=" C TRP B 229 " pdb=" CB TRP B 229 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" CG LEU A 92 " pdb=" CB LEU A 92 " pdb=" CD1 LEU A 92 " pdb=" CD2 LEU A 92 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CB ILE B 225 " pdb=" CA ILE B 225 " pdb=" CG1 ILE B 225 " pdb=" CG2 ILE B 225 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 759 not shown) Planarity restraints: 721 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 229 " -0.028 2.00e-02 2.50e+03 2.95e-02 2.17e+01 pdb=" CG TRP B 229 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP B 229 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP B 229 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 229 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 229 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 229 " -0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 229 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 229 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 229 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 229 " -0.016 2.00e-02 2.50e+03 1.95e-02 9.53e+00 pdb=" CG TRP A 229 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 229 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 229 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 229 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 229 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 229 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 229 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 229 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 229 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 252 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.18e+00 pdb=" N PRO A 253 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " 0.035 5.00e-02 4.00e+02 ... (remaining 718 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 714 2.76 - 3.30: 4279 3.30 - 3.83: 7391 3.83 - 4.37: 8110 4.37 - 4.90: 15202 Nonbonded interactions: 35696 Sorted by model distance: nonbonded pdb=" OG SER A 84 " pdb=" NH2 ARG A 144 " model vdw 2.227 3.120 nonbonded pdb=" OG SER B 58 " pdb=" OH TYR B 103 " model vdw 2.246 3.040 nonbonded pdb=" OG SER A 132 " pdb=" OD2 ASP A 176 " model vdw 2.320 3.040 nonbonded pdb=" O VAL A 298 " pdb=" OG1 THR A 302 " model vdw 2.329 3.040 nonbonded pdb=" OG1 THR A 202 " pdb=" OD1 ASP A 205 " model vdw 2.347 3.040 ... (remaining 35691 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' and (resid 44 through 111 or resid 115 through 327 or resid 601)) selection = (chain 'B' and (resid 44 through 151 or (resid 152 and (name N or name CA or nam \ e C or name O or name CB )) or resid 160 or (resid 161 and (name N or name CA or \ name C or name O or name CB )) or resid 162 through 327 or resid 601)) } 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: 5.510 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.340 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 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 : 0.007 0.200 4560 Z= 0.410 Angle : 0.799 14.077 6189 Z= 0.379 Chirality : 0.040 0.199 762 Planarity : 0.005 0.062 721 Dihedral : 14.107 87.807 1648 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.06 (0.35), residues: 555 helix: 2.86 (0.23), residues: 421 sheet: 1.83 (0.89), residues: 38 loop : -2.06 (0.56), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.003 TRP B 229 HIS 0.002 0.001 HIS A 214 PHE 0.011 0.001 PHE A 308 TYR 0.010 0.001 TYR B 103 ARG 0.003 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.475 Fit side-chains REVERT: A 79 ILE cc_start: 0.7930 (mm) cc_final: 0.7647 (mm) REVERT: A 199 MET cc_start: 0.7318 (ttm) cc_final: 0.6938 (ttm) REVERT: A 275 PHE cc_start: 0.8136 (t80) cc_final: 0.7924 (t80) REVERT: B 174 MET cc_start: 0.6158 (mmm) cc_final: 0.5737 (mmm) REVERT: B 193 GLN cc_start: 0.7231 (tt0) cc_final: 0.6882 (tt0) REVERT: B 283 SER cc_start: 0.8344 (m) cc_final: 0.8064 (t) REVERT: B 312 LEU cc_start: 0.7856 (mp) cc_final: 0.7587 (mt) outliers start: 0 outliers final: 1 residues processed: 81 average time/residue: 0.7347 time to fit residues: 63.5182 Evaluate side-chains 69 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 49 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN B 255 ASN B 256 GLN B 311 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 4560 Z= 0.370 Angle : 0.602 6.592 6189 Z= 0.313 Chirality : 0.044 0.179 762 Planarity : 0.005 0.052 721 Dihedral : 11.429 77.156 686 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.61 % Allowed : 7.85 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.17 (0.34), residues: 555 helix: 2.88 (0.22), residues: 432 sheet: 3.08 (0.98), residues: 27 loop : -2.26 (0.57), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 229 HIS 0.001 0.001 HIS B 214 PHE 0.023 0.002 PHE B 215 TYR 0.015 0.002 TYR B 280 ARG 0.006 0.001 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.507 Fit side-chains REVERT: A 79 ILE cc_start: 0.7807 (mm) cc_final: 0.7538 (mm) REVERT: A 195 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.6950 (pp) REVERT: A 200 THR cc_start: 0.7649 (m) cc_final: 0.7079 (p) REVERT: B 72 ILE cc_start: 0.8192 (mm) cc_final: 0.7933 (mt) REVERT: B 174 MET cc_start: 0.6309 (mmm) cc_final: 0.5851 (mmm) REVERT: B 193 GLN cc_start: 0.7270 (tt0) cc_final: 0.6911 (tt0) REVERT: B 199 MET cc_start: 0.6793 (mtm) cc_final: 0.6414 (mtm) REVERT: B 283 SER cc_start: 0.8391 (m) cc_final: 0.8167 (t) outliers start: 8 outliers final: 2 residues processed: 74 average time/residue: 0.5702 time to fit residues: 45.6819 Evaluate side-chains 68 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 195 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 13 optimal weight: 0.0970 chunk 50 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 chunk 17 optimal weight: 0.0870 chunk 40 optimal weight: 0.5980 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4560 Z= 0.266 Angle : 0.522 6.322 6189 Z= 0.284 Chirality : 0.041 0.170 762 Planarity : 0.005 0.053 721 Dihedral : 11.115 76.113 686 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.81 % Allowed : 9.05 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.30 (0.34), residues: 555 helix: 3.09 (0.22), residues: 429 sheet: 2.30 (1.50), residues: 12 loop : -1.73 (0.55), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 315 HIS 0.001 0.000 HIS A 214 PHE 0.026 0.002 PHE B 215 TYR 0.011 0.001 TYR B 280 ARG 0.005 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 0.485 Fit side-chains REVERT: A 79 ILE cc_start: 0.7812 (mm) cc_final: 0.7580 (mm) REVERT: A 195 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7161 (pp) REVERT: A 279 ARG cc_start: 0.8431 (tpp80) cc_final: 0.7837 (tpp-160) REVERT: B 72 ILE cc_start: 0.8179 (mm) cc_final: 0.7962 (mt) REVERT: B 174 MET cc_start: 0.6357 (mmm) cc_final: 0.5900 (mmm) REVERT: B 193 GLN cc_start: 0.7265 (tt0) cc_final: 0.6875 (tt0) REVERT: B 209 THR cc_start: 0.7926 (m) cc_final: 0.7668 (t) REVERT: B 210 SER cc_start: 0.7769 (m) cc_final: 0.7488 (t) REVERT: B 283 SER cc_start: 0.8375 (m) cc_final: 0.8157 (t) outliers start: 9 outliers final: 5 residues processed: 74 average time/residue: 0.5971 time to fit residues: 47.5125 Evaluate side-chains 69 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 266 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 0.2980 chunk 37 optimal weight: 0.0970 chunk 25 optimal weight: 0.4980 chunk 5 optimal weight: 0.1980 chunk 23 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 0.4980 chunk 26 optimal weight: 0.0770 chunk 47 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.2136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4560 Z= 0.189 Angle : 0.503 10.446 6189 Z= 0.266 Chirality : 0.039 0.189 762 Planarity : 0.005 0.056 721 Dihedral : 10.931 76.074 686 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.21 % Allowed : 10.87 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.66 (0.34), residues: 555 helix: 3.27 (0.22), residues: 431 sheet: 2.40 (0.94), residues: 24 loop : -1.78 (0.60), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 315 HIS 0.001 0.000 HIS A 214 PHE 0.029 0.001 PHE B 215 TYR 0.009 0.001 TYR A 280 ARG 0.002 0.000 ARG A 279 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 1.160 Fit side-chains REVERT: A 79 ILE cc_start: 0.7765 (mm) cc_final: 0.7515 (mm) REVERT: A 187 ASP cc_start: 0.7479 (p0) cc_final: 0.7227 (p0) REVERT: A 200 THR cc_start: 0.7543 (m) cc_final: 0.7079 (p) REVERT: A 279 ARG cc_start: 0.8452 (tpp80) cc_final: 0.7801 (tpp-160) REVERT: B 72 ILE cc_start: 0.8204 (mm) cc_final: 0.7884 (mt) REVERT: B 174 MET cc_start: 0.6346 (mmm) cc_final: 0.5892 (mmm) REVERT: B 193 GLN cc_start: 0.7248 (tt0) cc_final: 0.6883 (tt0) REVERT: B 199 MET cc_start: 0.6811 (mtm) cc_final: 0.6051 (mtt) REVERT: B 200 THR cc_start: 0.7190 (t) cc_final: 0.6626 (p) REVERT: B 207 SER cc_start: 0.7355 (OUTLIER) cc_final: 0.7033 (p) REVERT: B 209 THR cc_start: 0.7939 (m) cc_final: 0.7609 (t) REVERT: B 210 SER cc_start: 0.7800 (m) cc_final: 0.7483 (t) REVERT: B 283 SER cc_start: 0.8354 (m) cc_final: 0.8144 (t) outliers start: 11 outliers final: 2 residues processed: 74 average time/residue: 0.6149 time to fit residues: 49.1220 Evaluate side-chains 68 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 207 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 0.0980 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 0.0980 chunk 27 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4560 Z= 0.254 Angle : 0.534 10.408 6189 Z= 0.282 Chirality : 0.041 0.178 762 Planarity : 0.005 0.057 721 Dihedral : 11.011 77.765 684 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.21 % Allowed : 10.87 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.62 (0.33), residues: 555 helix: 3.26 (0.22), residues: 429 sheet: 2.44 (0.95), residues: 24 loop : -1.82 (0.59), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 284 HIS 0.001 0.000 HIS A 214 PHE 0.027 0.002 PHE B 215 TYR 0.011 0.001 TYR B 280 ARG 0.003 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.444 Fit side-chains REVERT: A 79 ILE cc_start: 0.7783 (mm) cc_final: 0.7549 (mm) REVERT: A 200 THR cc_start: 0.7500 (m) cc_final: 0.7096 (p) REVERT: A 279 ARG cc_start: 0.8475 (tpp80) cc_final: 0.7817 (tpp-160) REVERT: B 72 ILE cc_start: 0.8166 (mm) cc_final: 0.7932 (mt) REVERT: B 123 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.6112 (ptp-170) REVERT: B 174 MET cc_start: 0.6391 (mmm) cc_final: 0.5919 (mmm) REVERT: B 193 GLN cc_start: 0.7244 (tt0) cc_final: 0.6893 (tt0) REVERT: B 199 MET cc_start: 0.6856 (mtm) cc_final: 0.6429 (mtm) REVERT: B 209 THR cc_start: 0.7931 (m) cc_final: 0.7589 (t) REVERT: B 210 SER cc_start: 0.7839 (m) cc_final: 0.7523 (t) REVERT: B 283 SER cc_start: 0.8372 (m) cc_final: 0.8167 (t) outliers start: 11 outliers final: 6 residues processed: 70 average time/residue: 0.6385 time to fit residues: 47.8721 Evaluate side-chains 69 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 246 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 0.1980 chunk 31 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 53 optimal weight: 0.3980 chunk 44 optimal weight: 0.0980 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 0.2980 chunk 17 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.2380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4560 Z= 0.198 Angle : 0.518 10.836 6189 Z= 0.270 Chirality : 0.039 0.208 762 Planarity : 0.005 0.058 721 Dihedral : 10.887 77.352 684 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.81 % Allowed : 12.27 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.81 (0.33), residues: 555 helix: 3.33 (0.21), residues: 431 sheet: 2.69 (0.91), residues: 24 loop : -1.60 (0.61), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 315 HIS 0.001 0.000 HIS A 214 PHE 0.029 0.001 PHE B 215 TYR 0.009 0.001 TYR A 280 ARG 0.001 0.000 ARG A 279 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.499 Fit side-chains REVERT: A 122 THR cc_start: 0.8074 (t) cc_final: 0.7828 (p) REVERT: A 200 THR cc_start: 0.7499 (m) cc_final: 0.7101 (p) REVERT: B 123 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.6041 (ptp-170) REVERT: B 149 PHE cc_start: 0.7093 (m-80) cc_final: 0.5824 (t80) REVERT: B 174 MET cc_start: 0.6381 (mmm) cc_final: 0.5906 (mmm) REVERT: B 193 GLN cc_start: 0.7240 (tt0) cc_final: 0.6883 (tt0) REVERT: B 199 MET cc_start: 0.6871 (mtm) cc_final: 0.6466 (mtm) REVERT: B 210 SER cc_start: 0.7827 (m) cc_final: 0.7462 (t) REVERT: B 283 SER cc_start: 0.8360 (m) cc_final: 0.8154 (t) outliers start: 9 outliers final: 1 residues processed: 70 average time/residue: 0.7089 time to fit residues: 52.9028 Evaluate side-chains 67 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 195 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 0.0980 chunk 30 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 44 optimal weight: 0.0980 chunk 29 optimal weight: 0.2980 chunk 53 optimal weight: 0.0010 chunk 33 optimal weight: 0.2980 chunk 32 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 31 optimal weight: 0.3980 overall best weight: 0.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4560 Z= 0.159 Angle : 0.488 9.431 6189 Z= 0.259 Chirality : 0.039 0.216 762 Planarity : 0.005 0.059 721 Dihedral : 10.768 76.974 684 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.81 % Allowed : 12.27 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.96 (0.33), residues: 555 helix: 3.42 (0.21), residues: 431 sheet: 2.85 (0.89), residues: 24 loop : -1.49 (0.62), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 315 HIS 0.001 0.000 HIS A 214 PHE 0.030 0.001 PHE B 215 TYR 0.008 0.001 TYR A 280 ARG 0.002 0.000 ARG A 279 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.557 Fit side-chains REVERT: A 200 THR cc_start: 0.7496 (m) cc_final: 0.7114 (p) REVERT: A 279 ARG cc_start: 0.8390 (tpp80) cc_final: 0.7992 (ttm170) REVERT: B 123 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.6032 (ptp-170) REVERT: B 149 PHE cc_start: 0.7057 (m-80) cc_final: 0.5812 (t80) REVERT: B 174 MET cc_start: 0.6423 (mmm) cc_final: 0.5948 (mmm) REVERT: B 193 GLN cc_start: 0.7238 (tt0) cc_final: 0.6880 (tt0) REVERT: B 199 MET cc_start: 0.6845 (mtm) cc_final: 0.6289 (mtm) REVERT: B 210 SER cc_start: 0.7842 (m) cc_final: 0.7474 (t) outliers start: 9 outliers final: 3 residues processed: 69 average time/residue: 0.7093 time to fit residues: 52.3701 Evaluate side-chains 72 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 246 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.0370 chunk 33 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 0.0970 chunk 4 optimal weight: 0.5980 chunk 41 optimal weight: 0.0670 chunk 48 optimal weight: 0.0980 chunk 50 optimal weight: 0.8980 chunk 46 optimal weight: 0.4980 chunk 49 optimal weight: 0.1980 overall best weight: 0.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4560 Z= 0.137 Angle : 0.502 12.288 6189 Z= 0.257 Chirality : 0.038 0.180 762 Planarity : 0.005 0.060 721 Dihedral : 10.474 75.664 684 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.41 % Allowed : 13.68 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.09 (0.33), residues: 555 helix: 3.49 (0.21), residues: 430 sheet: 3.08 (0.86), residues: 24 loop : -1.36 (0.62), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 284 HIS 0.001 0.000 HIS A 214 PHE 0.029 0.001 PHE B 215 TYR 0.008 0.001 TYR A 280 ARG 0.002 0.000 ARG A 279 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 0.523 Fit side-chains REVERT: A 79 ILE cc_start: 0.7762 (mm) cc_final: 0.7546 (mm) REVERT: A 200 THR cc_start: 0.7446 (m) cc_final: 0.7063 (p) REVERT: A 279 ARG cc_start: 0.8399 (tpp80) cc_final: 0.8123 (tpp-160) REVERT: B 149 PHE cc_start: 0.7017 (m-80) cc_final: 0.5789 (t80) REVERT: B 174 MET cc_start: 0.6437 (mmm) cc_final: 0.5931 (mmm) REVERT: B 193 GLN cc_start: 0.7218 (tt0) cc_final: 0.6874 (tt0) REVERT: B 199 MET cc_start: 0.6866 (mtm) cc_final: 0.6536 (mtm) REVERT: B 210 SER cc_start: 0.7812 (m) cc_final: 0.7459 (t) outliers start: 7 outliers final: 3 residues processed: 72 average time/residue: 0.6918 time to fit residues: 53.2507 Evaluate side-chains 70 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 246 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 0.3980 chunk 29 optimal weight: 0.0870 chunk 21 optimal weight: 0.1980 chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 46 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 chunk 52 optimal weight: 0.3980 chunk 31 optimal weight: 0.0980 overall best weight: 0.2358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4560 Z= 0.195 Angle : 0.512 9.179 6189 Z= 0.268 Chirality : 0.040 0.232 762 Planarity : 0.005 0.061 721 Dihedral : 10.498 78.315 684 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.01 % Allowed : 14.29 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.03 (0.33), residues: 555 helix: 3.44 (0.21), residues: 431 sheet: 3.03 (0.83), residues: 24 loop : -1.36 (0.62), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 284 HIS 0.001 0.000 HIS B 73 PHE 0.030 0.001 PHE B 215 TYR 0.009 0.001 TYR B 280 ARG 0.008 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.487 Fit side-chains REVERT: A 200 THR cc_start: 0.7464 (m) cc_final: 0.7073 (p) REVERT: B 149 PHE cc_start: 0.6957 (m-80) cc_final: 0.5743 (t80) REVERT: B 174 MET cc_start: 0.6469 (mmm) cc_final: 0.5979 (mmm) REVERT: B 193 GLN cc_start: 0.7216 (tt0) cc_final: 0.6867 (tt0) REVERT: B 199 MET cc_start: 0.6886 (mtm) cc_final: 0.6570 (mtm) REVERT: B 210 SER cc_start: 0.7798 (m) cc_final: 0.7439 (t) outliers start: 5 outliers final: 4 residues processed: 68 average time/residue: 0.6508 time to fit residues: 47.5377 Evaluate side-chains 70 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 246 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 0.1980 chunk 36 optimal weight: 0.2980 chunk 54 optimal weight: 0.0870 chunk 50 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 33 optimal weight: 0.2980 chunk 26 optimal weight: 0.0980 chunk 34 optimal weight: 0.0970 chunk 46 optimal weight: 0.1980 chunk 13 optimal weight: 0.4980 overall best weight: 0.1356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4560 Z= 0.149 Angle : 0.511 11.923 6189 Z= 0.261 Chirality : 0.038 0.183 762 Planarity : 0.005 0.060 721 Dihedral : 10.372 77.251 684 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.21 % Allowed : 14.49 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.10 (0.33), residues: 555 helix: 3.49 (0.21), residues: 430 sheet: 3.08 (0.84), residues: 24 loop : -1.30 (0.62), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 284 HIS 0.001 0.000 HIS A 214 PHE 0.030 0.001 PHE B 215 TYR 0.008 0.001 TYR A 280 ARG 0.007 0.000 ARG B 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.471 Fit side-chains REVERT: A 200 THR cc_start: 0.7454 (m) cc_final: 0.7077 (p) REVERT: A 279 ARG cc_start: 0.8454 (tpp80) cc_final: 0.8092 (tpp-160) REVERT: B 149 PHE cc_start: 0.6945 (m-80) cc_final: 0.5708 (t80) REVERT: B 174 MET cc_start: 0.6508 (mmm) cc_final: 0.5972 (mmm) REVERT: B 193 GLN cc_start: 0.7206 (tt0) cc_final: 0.6868 (tt0) REVERT: B 199 MET cc_start: 0.6883 (mtm) cc_final: 0.6583 (mtm) REVERT: B 210 SER cc_start: 0.7777 (m) cc_final: 0.7426 (t) outliers start: 6 outliers final: 5 residues processed: 67 average time/residue: 0.6995 time to fit residues: 50.1887 Evaluate side-chains 72 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 246 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 0.2980 chunk 6 optimal weight: 0.0570 chunk 12 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 5 optimal weight: 0.0970 chunk 8 optimal weight: 0.0770 chunk 38 optimal weight: 0.7980 chunk 2 optimal weight: 0.1980 chunk 31 optimal weight: 0.7980 overall best weight: 0.1454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.137556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.117558 restraints weight = 5651.640| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.85 r_work: 0.3499 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4560 Z= 0.154 Angle : 0.512 9.550 6189 Z= 0.262 Chirality : 0.039 0.242 762 Planarity : 0.005 0.061 721 Dihedral : 10.351 77.145 684 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.21 % Allowed : 14.49 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.13 (0.33), residues: 555 helix: 3.49 (0.21), residues: 431 sheet: 3.15 (0.83), residues: 24 loop : -1.25 (0.63), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 284 HIS 0.001 0.000 HIS A 214 PHE 0.030 0.001 PHE B 215 TYR 0.008 0.001 TYR A 280 ARG 0.007 0.000 ARG B 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1932.94 seconds wall clock time: 35 minutes 1.00 seconds (2101.00 seconds total)