Starting phenix.real_space_refine on Mon Sep 23 14:57:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeo_13935/09_2024/7qeo_13935.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeo_13935/09_2024/7qeo_13935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeo_13935/09_2024/7qeo_13935.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeo_13935/09_2024/7qeo_13935.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeo_13935/09_2024/7qeo_13935.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeo_13935/09_2024/7qeo_13935.cif" } resolution = 2.9 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 2045 2.51 5 N 481 2.21 5 O 502 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3056 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1514 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Chain breaks: 1 Chain: "B" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1481 Classifications: {'peptide': 182} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 175} Chain breaks: 1 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {'LMT': 2, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 27 Unusual residues: {'LMT': 2, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.49, per 1000 atoms: 0.81 Number of scatterers: 3056 At special positions: 0 Unit cell: (69.76, 66.49, 89.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 502 8.00 N 481 7.00 C 2045 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 169 " 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: 0.89 Conformation dependent library (CDL) restraints added in 490.5 milliseconds 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 704 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 2 sheets defined 77.2% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 5 through 14 Processing helix chain 'A' and resid 18 through 39 removed outlier: 4.275A pdb=" N LEU A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N THR A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 47 removed outlier: 4.109A pdb=" N TRP A 44 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY A 45 " --> pdb=" O GLU A 42 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASP A 46 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A 47 " --> pdb=" O TRP A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 72 through 100 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 130 through 159 removed outlier: 3.822A pdb=" N VAL A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 155 " --> pdb=" O MET A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 217 removed outlier: 4.237A pdb=" N ARG A 216 " --> pdb=" O TYR A 212 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 13 Processing helix chain 'B' and resid 18 through 39 removed outlier: 3.773A pdb=" N ILE B 23 " --> pdb=" O SER B 19 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LEU B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N THR B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 44 removed outlier: 4.031A pdb=" N VAL B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 39 through 44' Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 72 through 100 Proline residue: B 87 - end of helix removed outlier: 3.655A pdb=" N TYR B 97 " --> pdb=" O MET B 93 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ARG B 98 " --> pdb=" O HIS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 159 removed outlier: 3.545A pdb=" N ARG B 143 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL B 144 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B 145 " --> pdb=" O PHE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53 212 hydrogen bonds defined for protein. 621 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: 0.68 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 885 1.34 - 1.46: 668 1.46 - 1.57: 1539 1.57 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 3132 Sorted by residual: bond pdb=" C1 LMT A 301 " pdb=" C2 LMT A 301 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.05e+00 bond pdb=" C1 LMT B 302 " pdb=" C2 LMT B 302 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 5.95e+00 bond pdb=" C7 LMT A 302 " pdb=" C8 LMT A 302 " ideal model delta sigma weight residual 1.529 1.567 -0.038 2.00e-02 2.50e+03 3.55e+00 bond pdb=" C7 LMT B 302 " pdb=" C8 LMT B 302 " ideal model delta sigma weight residual 1.529 1.565 -0.036 2.00e-02 2.50e+03 3.26e+00 bond pdb=" C7 LMT A 301 " pdb=" C8 LMT A 301 " ideal model delta sigma weight residual 1.529 1.565 -0.036 2.00e-02 2.50e+03 3.26e+00 ... (remaining 3127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 4080 1.56 - 3.12: 106 3.12 - 4.69: 31 4.69 - 6.25: 16 6.25 - 7.81: 7 Bond angle restraints: 4240 Sorted by residual: angle pdb=" C ARG B 184 " pdb=" CA ARG B 184 " pdb=" CB ARG B 184 " ideal model delta sigma weight residual 111.00 108.36 2.64 8.70e-01 1.32e+00 9.18e+00 angle pdb=" C6 LMT A 302 " pdb=" C7 LMT A 302 " pdb=" C8 LMT A 302 " ideal model delta sigma weight residual 117.26 109.45 7.81 3.00e+00 1.11e-01 6.78e+00 angle pdb=" C6 LMT B 302 " pdb=" C7 LMT B 302 " pdb=" C8 LMT B 302 " ideal model delta sigma weight residual 117.26 109.76 7.50 3.00e+00 1.11e-01 6.24e+00 angle pdb=" C2 LMT B 302 " pdb=" C3 LMT B 302 " pdb=" C4 LMT B 302 " ideal model delta sigma weight residual 117.09 109.70 7.39 3.00e+00 1.11e-01 6.07e+00 angle pdb=" C7 LMT B 302 " pdb=" C8 LMT B 302 " pdb=" C9 LMT B 302 " ideal model delta sigma weight residual 116.37 109.08 7.29 3.00e+00 1.11e-01 5.91e+00 ... (remaining 4235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.51: 1588 14.51 - 29.01: 163 29.01 - 43.52: 45 43.52 - 58.03: 17 58.03 - 72.53: 1 Dihedral angle restraints: 1814 sinusoidal: 728 harmonic: 1086 Sorted by residual: dihedral pdb=" CA PRO B 175 " pdb=" C PRO B 175 " pdb=" N ASN B 176 " pdb=" CA ASN B 176 " ideal model delta harmonic sigma weight residual 180.00 -159.50 -20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA PRO A 175 " pdb=" C PRO A 175 " pdb=" N ASN A 176 " pdb=" CA ASN A 176 " ideal model delta harmonic sigma weight residual -180.00 -160.16 -19.84 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA ILE A 23 " pdb=" C ILE A 23 " pdb=" N TRP A 24 " pdb=" CA TRP A 24 " ideal model delta harmonic sigma weight residual -180.00 -161.10 -18.90 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 1811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 277 0.032 - 0.063: 149 0.063 - 0.095: 36 0.095 - 0.126: 18 0.126 - 0.158: 2 Chirality restraints: 482 Sorted by residual: chirality pdb=" CA THR A 86 " pdb=" N THR A 86 " pdb=" C THR A 86 " pdb=" CB THR A 86 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CA THR B 86 " pdb=" N THR B 86 " pdb=" C THR B 86 " pdb=" CB THR B 86 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA PRO B 173 " pdb=" N PRO B 173 " pdb=" C PRO B 173 " pdb=" CB PRO B 173 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.85e-01 ... (remaining 479 not shown) Planarity restraints: 504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 174 " 0.019 5.00e-02 4.00e+02 2.89e-02 1.34e+00 pdb=" N PRO A 175 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 175 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 175 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 174 " -0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO B 175 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 175 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 175 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 133 " -0.006 2.00e-02 2.50e+03 6.53e-03 1.07e+00 pdb=" CG TRP B 133 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP B 133 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP B 133 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 133 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 133 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 133 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 133 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 133 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 133 " 0.000 2.00e-02 2.50e+03 ... (remaining 501 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 32 2.66 - 3.22: 2948 3.22 - 3.78: 4396 3.78 - 4.34: 5824 4.34 - 4.90: 9781 Nonbonded interactions: 22981 Sorted by model distance: nonbonded pdb=" O ILE B 71 " pdb=" OH TYR B 158 " model vdw 2.106 3.040 nonbonded pdb=" OH TYR A 68 " pdb=" O LYS A 168 " model vdw 2.181 3.040 nonbonded pdb=" OH TYR B 68 " pdb=" O LYS B 168 " model vdw 2.244 3.040 nonbonded pdb=" O ILE A 71 " pdb=" OH TYR A 158 " model vdw 2.284 3.040 nonbonded pdb=" O THR B 135 " pdb=" OG SER B 138 " model vdw 2.322 3.040 ... (remaining 22976 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 8 through 101 or resid 130 through 217 or (resid 301 and ( \ name C5 or name C6 or name C7 )) or resid 302 or (resid 303 and (name C11 or nam \ e C12 or name C13 or name C14 or name C15 or name C18 or name C19 or name C20 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C8 )))) selection = (chain 'B' and (resid 8 through 217 or resid 301 or (resid 302 and (name C4 or n \ ame C5 or name C6 or name C7 or name C8 )) or (resid 303 and (name C11 or name C \ 12 or name C13 or name C14 or name C15 or name C18 or name C19 or name C20 or na \ me C21 or name C22 or name C23 or name C24 or name C25 or name C8 )))) } 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: 0.660 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: 0.040 Set scattering table: 0.080 Process input model: 12.450 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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:12.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 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 0.049 3132 Z= 0.449 Angle : 0.776 7.810 4240 Z= 0.376 Chirality : 0.042 0.158 482 Planarity : 0.003 0.029 504 Dihedral : 13.539 72.532 1092 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.61 (0.43), residues: 360 helix: 0.97 (0.32), residues: 241 sheet: 0.95 (1.04), residues: 22 loop : -1.00 (0.64), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 133 HIS 0.002 0.001 HIS B 94 PHE 0.009 0.001 PHE A 181 TYR 0.012 0.002 TYR A 212 ARG 0.003 0.001 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.340 Fit side-chains REVERT: B 89 LEU cc_start: 0.9403 (tt) cc_final: 0.9182 (tm) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 1.1941 time to fit residues: 57.7442 Evaluate side-chains 40 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 0.4980 chunk 27 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.0970 chunk 18 optimal weight: 20.0000 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8637 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3132 Z= 0.208 Angle : 0.630 7.454 4240 Z= 0.344 Chirality : 0.043 0.146 482 Planarity : 0.004 0.029 504 Dihedral : 8.248 52.468 431 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.91 % Allowed : 9.70 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.83 (0.44), residues: 360 helix: 2.12 (0.32), residues: 244 sheet: 1.37 (1.09), residues: 22 loop : -1.32 (0.62), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 133 HIS 0.002 0.001 HIS A 94 PHE 0.012 0.002 PHE A 150 TYR 0.017 0.002 TYR A 212 ARG 0.006 0.001 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.404 Fit side-chains REVERT: A 41 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8196 (tttt) REVERT: B 22 LYS cc_start: 0.8620 (mmtt) cc_final: 0.8260 (mmmt) outliers start: 3 outliers final: 1 residues processed: 47 average time/residue: 1.3028 time to fit residues: 62.8808 Evaluate side-chains 46 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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: 0.8674 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 3132 Z= 0.372 Angle : 0.638 5.923 4240 Z= 0.344 Chirality : 0.045 0.171 482 Planarity : 0.004 0.031 504 Dihedral : 8.121 56.486 431 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.42 % Allowed : 12.42 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.44), residues: 360 helix: 2.31 (0.32), residues: 246 sheet: 1.31 (1.09), residues: 22 loop : -1.34 (0.63), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 133 HIS 0.002 0.001 HIS A 73 PHE 0.030 0.002 PHE B 29 TYR 0.014 0.002 TYR B 68 ARG 0.006 0.001 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.368 Fit side-chains REVERT: A 41 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8342 (tttt) REVERT: A 216 ARG cc_start: 0.8171 (mtm180) cc_final: 0.7932 (ptp-110) REVERT: B 22 LYS cc_start: 0.8607 (mmtt) cc_final: 0.8060 (mmtt) outliers start: 8 outliers final: 3 residues processed: 50 average time/residue: 1.2721 time to fit residues: 65.4904 Evaluate side-chains 49 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 182 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.8623 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3132 Z= 0.197 Angle : 0.587 7.955 4240 Z= 0.312 Chirality : 0.041 0.167 482 Planarity : 0.004 0.031 504 Dihedral : 7.621 57.884 431 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.21 % Allowed : 15.15 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.45), residues: 360 helix: 2.55 (0.32), residues: 247 sheet: 1.51 (1.12), residues: 22 loop : -1.45 (0.64), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 133 HIS 0.003 0.001 HIS B 94 PHE 0.035 0.001 PHE B 29 TYR 0.010 0.001 TYR A 212 ARG 0.006 0.001 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.347 Fit side-chains REVERT: A 41 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8127 (tttt) REVERT: A 216 ARG cc_start: 0.8195 (mtm180) cc_final: 0.7804 (ptp-110) outliers start: 4 outliers final: 1 residues processed: 46 average time/residue: 1.2921 time to fit residues: 61.2100 Evaluate side-chains 45 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 97 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 20.0000 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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: 0.8625 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3132 Z= 0.218 Angle : 0.567 7.408 4240 Z= 0.302 Chirality : 0.041 0.159 482 Planarity : 0.003 0.030 504 Dihedral : 7.146 53.699 431 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.82 % Allowed : 15.45 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.45), residues: 360 helix: 2.72 (0.32), residues: 247 sheet: 1.60 (1.13), residues: 22 loop : -1.53 (0.64), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 133 HIS 0.002 0.001 HIS B 94 PHE 0.010 0.001 PHE A 194 TYR 0.013 0.001 TYR B 158 ARG 0.003 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.313 Fit side-chains REVERT: A 216 ARG cc_start: 0.8111 (mtm180) cc_final: 0.7826 (ptp-110) outliers start: 6 outliers final: 3 residues processed: 50 average time/residue: 1.0962 time to fit residues: 56.5202 Evaluate side-chains 47 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 182 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.8605 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3132 Z= 0.186 Angle : 0.550 7.718 4240 Z= 0.292 Chirality : 0.041 0.156 482 Planarity : 0.003 0.031 504 Dihedral : 6.546 54.654 431 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.82 % Allowed : 17.27 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.46), residues: 360 helix: 2.88 (0.32), residues: 247 sheet: 1.72 (1.15), residues: 22 loop : -1.63 (0.63), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 133 HIS 0.002 0.000 HIS A 73 PHE 0.037 0.001 PHE B 29 TYR 0.007 0.001 TYR B 158 ARG 0.004 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.374 Fit side-chains REVERT: A 216 ARG cc_start: 0.8061 (mtm180) cc_final: 0.7769 (ptp-110) outliers start: 6 outliers final: 3 residues processed: 53 average time/residue: 1.0474 time to fit residues: 57.2852 Evaluate side-chains 47 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain B residue 212 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 0.0670 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- 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: 0.8596 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3132 Z= 0.188 Angle : 0.613 8.073 4240 Z= 0.313 Chirality : 0.041 0.154 482 Planarity : 0.003 0.030 504 Dihedral : 6.227 57.129 431 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.82 % Allowed : 18.18 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.45), residues: 360 helix: 2.84 (0.32), residues: 246 sheet: 1.70 (1.15), residues: 22 loop : -1.54 (0.62), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 133 HIS 0.002 0.000 HIS A 73 PHE 0.011 0.001 PHE A 194 TYR 0.006 0.001 TYR B 68 ARG 0.004 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.347 Fit side-chains REVERT: A 216 ARG cc_start: 0.8035 (mtm180) cc_final: 0.7784 (ptp-110) outliers start: 6 outliers final: 3 residues processed: 49 average time/residue: 1.0975 time to fit residues: 55.4820 Evaluate side-chains 48 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain B residue 212 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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: 0.8633 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3132 Z= 0.272 Angle : 0.629 8.931 4240 Z= 0.323 Chirality : 0.043 0.154 482 Planarity : 0.004 0.029 504 Dihedral : 6.316 59.222 431 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.12 % Allowed : 19.09 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.45), residues: 360 helix: 2.84 (0.32), residues: 246 sheet: 1.59 (1.12), residues: 22 loop : -1.45 (0.64), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 133 HIS 0.002 0.001 HIS A 73 PHE 0.038 0.001 PHE B 29 TYR 0.009 0.001 TYR B 68 ARG 0.004 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.351 Fit side-chains REVERT: A 216 ARG cc_start: 0.8053 (mtm180) cc_final: 0.7770 (ptp-110) REVERT: B 29 PHE cc_start: 0.8654 (t80) cc_final: 0.8346 (t80) outliers start: 7 outliers final: 5 residues processed: 50 average time/residue: 1.1678 time to fit residues: 60.1722 Evaluate side-chains 49 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 212 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.8618 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 3132 Z= 0.241 Angle : 0.630 8.608 4240 Z= 0.325 Chirality : 0.042 0.152 482 Planarity : 0.004 0.031 504 Dihedral : 6.098 56.513 431 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.82 % Allowed : 19.39 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.45), residues: 360 helix: 2.82 (0.32), residues: 245 sheet: 1.63 (1.13), residues: 22 loop : -1.57 (0.64), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 133 HIS 0.002 0.000 HIS A 73 PHE 0.052 0.001 PHE B 29 TYR 0.008 0.001 TYR B 68 ARG 0.003 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.392 Fit side-chains REVERT: A 216 ARG cc_start: 0.8035 (mtm180) cc_final: 0.7772 (ptp-110) outliers start: 6 outliers final: 5 residues processed: 50 average time/residue: 1.2307 time to fit residues: 63.2990 Evaluate side-chains 49 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain B residue 212 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.8606 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 3132 Z= 0.224 Angle : 0.654 8.967 4240 Z= 0.335 Chirality : 0.042 0.155 482 Planarity : 0.004 0.030 504 Dihedral : 5.799 52.268 431 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.21 % Allowed : 20.61 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.46), residues: 360 helix: 2.80 (0.32), residues: 246 sheet: 1.68 (1.14), residues: 22 loop : -1.64 (0.65), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 133 HIS 0.002 0.000 HIS A 73 PHE 0.009 0.001 PHE B 29 TYR 0.007 0.001 TYR B 68 ARG 0.004 0.000 ARG B 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.374 Fit side-chains REVERT: A 216 ARG cc_start: 0.8017 (mtm180) cc_final: 0.7784 (ptp-110) REVERT: B 216 ARG cc_start: 0.7923 (tpm-80) cc_final: 0.7370 (tpt90) outliers start: 4 outliers final: 4 residues processed: 49 average time/residue: 1.2875 time to fit residues: 64.8544 Evaluate side-chains 50 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain B residue 212 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 0.0670 chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.7918 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.081583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.058498 restraints weight = 8412.117| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.52 r_work: 0.2780 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 3132 Z= 0.214 Angle : 0.636 8.992 4240 Z= 0.324 Chirality : 0.041 0.150 482 Planarity : 0.003 0.030 504 Dihedral : 5.532 49.145 431 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.52 % Allowed : 20.00 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.46), residues: 360 helix: 2.82 (0.32), residues: 246 sheet: 1.70 (1.14), residues: 22 loop : -1.67 (0.64), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 133 HIS 0.002 0.000 HIS A 73 PHE 0.038 0.001 PHE B 29 TYR 0.007 0.001 TYR B 68 ARG 0.003 0.000 ARG B 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1508.18 seconds wall clock time: 27 minutes 15.99 seconds (1635.99 seconds total)