Starting phenix.real_space_refine on Tue Feb 11 00:49:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qeo_13935/02_2025/7qeo_13935.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qeo_13935/02_2025/7qeo_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/cci-nas-00/data/ceres_data/7qeo_13935/02_2025/7qeo_13935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qeo_13935/02_2025/7qeo_13935.map" model { file = "/net/cci-nas-00/data/ceres_data/7qeo_13935/02_2025/7qeo_13935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qeo_13935/02_2025/7qeo_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-5592/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: 2.86, per 1000 atoms: 0.94 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: 0.87 Conformation dependent library (CDL) restraints added in 358.4 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: 0.28 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: 0.78 Time building geometry restraints manager: 0.98 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: 0.270 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.800 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:13.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.130 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.486 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: 1.4203 time to fit residues: 68.7344 Evaluate side-chains 40 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.080209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.057115 restraints weight = 8267.680| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.48 r_work: 0.2746 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 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 to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.329 Fit side-chains REVERT: A 41 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8492 (tttt) REVERT: B 22 LYS cc_start: 0.8653 (mmtt) cc_final: 0.8298 (mmmt) REVERT: B 143 ARG cc_start: 0.8523 (mtt90) cc_final: 0.8315 (mtt90) outliers start: 3 outliers final: 1 residues processed: 47 average time/residue: 1.3741 time to fit residues: 66.3017 Evaluate side-chains 46 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 5 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 12 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3469 r_free = 0.3469 target = 0.080591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.057778 restraints weight = 8256.393| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.45 r_work: 0.2762 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3132 Z= 0.214 Angle : 0.574 6.732 4240 Z= 0.307 Chirality : 0.042 0.163 482 Planarity : 0.004 0.028 504 Dihedral : 7.708 57.634 431 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.52 % Allowed : 12.73 % Favored : 85.76 % 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: 2.25 (0.45), residues: 360 helix: 2.40 (0.32), residues: 251 sheet: 1.55 (1.11), residues: 22 loop : -1.36 (0.66), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 133 HIS 0.001 0.001 HIS B 73 PHE 0.032 0.001 PHE B 29 TYR 0.012 0.002 TYR A 152 ARG 0.004 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 50 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.373 Fit side-chains REVERT: A 41 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8490 (tttt) REVERT: A 216 ARG cc_start: 0.8291 (mtm180) cc_final: 0.7794 (ptt-90) REVERT: B 159 ASP cc_start: 0.9037 (t0) cc_final: 0.8821 (p0) outliers start: 5 outliers final: 1 residues processed: 47 average time/residue: 1.3455 time to fit residues: 64.9675 Evaluate side-chains 46 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 93 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 13 optimal weight: 0.0980 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.081682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.058919 restraints weight = 8398.362| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.48 r_work: 0.2791 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3132 Z= 0.170 Angle : 0.560 8.361 4240 Z= 0.298 Chirality : 0.040 0.162 482 Planarity : 0.003 0.028 504 Dihedral : 7.151 57.263 431 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.52 % Allowed : 15.15 % Favored : 83.33 % 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: 2.30 (0.45), residues: 360 helix: 2.52 (0.33), residues: 247 sheet: 1.73 (1.15), residues: 22 loop : -1.50 (0.63), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 133 HIS 0.001 0.000 HIS B 73 PHE 0.009 0.001 PHE A 29 TYR 0.009 0.001 TYR A 212 ARG 0.006 0.000 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 54 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.380 Fit side-chains REVERT: A 15 LYS cc_start: 0.6455 (mmtm) cc_final: 0.6238 (mmpt) REVERT: A 216 ARG cc_start: 0.8370 (mtm180) cc_final: 0.7949 (ptp-110) outliers start: 5 outliers final: 0 residues processed: 50 average time/residue: 1.3046 time to fit residues: 67.0934 Evaluate side-chains 45 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 14 optimal weight: 0.1980 chunk 10 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- 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 = 0.3443 r_free = 0.3443 target = 0.079152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.056207 restraints weight = 8308.554| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.45 r_work: 0.2724 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3132 Z= 0.356 Angle : 0.627 6.854 4240 Z= 0.331 Chirality : 0.044 0.153 482 Planarity : 0.004 0.030 504 Dihedral : 7.318 55.746 431 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.42 % Allowed : 15.76 % Favored : 81.82 % 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: 2.25 (0.45), residues: 360 helix: 2.46 (0.32), residues: 247 sheet: 1.46 (1.09), residues: 22 loop : -1.38 (0.65), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 133 HIS 0.002 0.001 HIS A 73 PHE 0.036 0.002 PHE B 29 TYR 0.013 0.002 TYR B 158 ARG 0.002 0.001 ARG B 75 *********************** 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 51 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.334 Fit side-chains REVERT: A 216 ARG cc_start: 0.8366 (mtm180) cc_final: 0.7992 (ptp-110) outliers start: 8 outliers final: 4 residues processed: 48 average time/residue: 1.2300 time to fit residues: 60.8536 Evaluate side-chains 47 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 0.0980 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.081529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.058341 restraints weight = 8602.872| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.54 r_work: 0.2779 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3132 Z= 0.175 Angle : 0.562 7.987 4240 Z= 0.296 Chirality : 0.041 0.152 482 Planarity : 0.003 0.030 504 Dihedral : 6.749 52.174 431 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.12 % Allowed : 16.06 % Favored : 81.82 % 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: 2.43 (0.46), residues: 360 helix: 2.67 (0.33), residues: 247 sheet: 1.66 (1.13), residues: 22 loop : -1.59 (0.63), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 133 HIS 0.002 0.000 HIS A 73 PHE 0.008 0.001 PHE B 31 TYR 0.007 0.001 TYR A 212 ARG 0.003 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 53 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.327 Fit side-chains REVERT: A 15 LYS cc_start: 0.6544 (mmtm) cc_final: 0.6315 (mmpt) REVERT: A 216 ARG cc_start: 0.8279 (mtm180) cc_final: 0.7903 (ptp-110) outliers start: 7 outliers final: 3 residues processed: 51 average time/residue: 1.1526 time to fit residues: 60.5587 Evaluate side-chains 48 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 13 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 7 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3471 r_free = 0.3471 target = 0.080729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.057598 restraints weight = 8397.980| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.46 r_work: 0.2763 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2684 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= 0.248 Angle : 0.602 7.932 4240 Z= 0.313 Chirality : 0.043 0.152 482 Planarity : 0.004 0.029 504 Dihedral : 6.633 54.450 431 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.42 % Allowed : 16.36 % Favored : 81.21 % 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: 2.35 (0.45), residues: 360 helix: 2.58 (0.33), residues: 246 sheet: 1.63 (1.12), residues: 22 loop : -1.46 (0.64), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 133 HIS 0.002 0.001 HIS A 73 PHE 0.033 0.001 PHE B 29 TYR 0.008 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 54 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.337 Fit side-chains REVERT: A 15 LYS cc_start: 0.6609 (mmtm) cc_final: 0.6348 (mmpt) REVERT: A 216 ARG cc_start: 0.8340 (mtm180) cc_final: 0.7936 (ptp-110) outliers start: 8 outliers final: 5 residues processed: 53 average time/residue: 1.2337 time to fit residues: 67.3346 Evaluate side-chains 50 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.081195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.058171 restraints weight = 8421.300| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.49 r_work: 0.2775 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3132 Z= 0.208 Angle : 0.628 8.510 4240 Z= 0.322 Chirality : 0.042 0.153 482 Planarity : 0.004 0.030 504 Dihedral : 6.398 56.271 431 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.57 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: 2.36 (0.45), residues: 360 helix: 2.59 (0.33), residues: 246 sheet: 1.67 (1.13), residues: 22 loop : -1.50 (0.63), 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 0.013 0.001 PHE A 194 TYR 0.007 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 53 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.339 Fit side-chains REVERT: A 15 LYS cc_start: 0.6561 (mmtm) cc_final: 0.6299 (mmpt) REVERT: A 216 ARG cc_start: 0.8323 (mtm180) cc_final: 0.7941 (ptp-110) REVERT: B 216 ARG cc_start: 0.8304 (tpm-80) cc_final: 0.7753 (tpt90) outliers start: 6 outliers final: 3 residues processed: 51 average time/residue: 1.2754 time to fit residues: 66.9316 Evaluate side-chains 49 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 15 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.081495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.058452 restraints weight = 8321.821| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.47 r_work: 0.2781 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 3132 Z= 0.224 Angle : 0.624 8.253 4240 Z= 0.324 Chirality : 0.042 0.153 482 Planarity : 0.004 0.030 504 Dihedral : 6.171 59.077 431 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.52 % Allowed : 18.79 % Favored : 79.70 % 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: 2.34 (0.46), residues: 360 helix: 2.62 (0.33), residues: 244 sheet: 1.74 (1.14), residues: 22 loop : -1.57 (0.63), residues: 94 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 0.054 0.002 PHE B 29 TYR 0.007 0.001 TYR B 158 ARG 0.005 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 to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.358 Fit side-chains REVERT: A 15 LYS cc_start: 0.6497 (mmtm) cc_final: 0.6265 (mmpt) REVERT: A 216 ARG cc_start: 0.8312 (mtm180) cc_final: 0.7944 (ptp-110) outliers start: 5 outliers final: 4 residues processed: 51 average time/residue: 1.2638 time to fit residues: 66.2533 Evaluate side-chains 50 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 212 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3478 r_free = 0.3478 target = 0.081548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.058588 restraints weight = 8277.635| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.45 r_work: 0.2777 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2999 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= 0.222 Angle : 0.639 8.951 4240 Z= 0.329 Chirality : 0.041 0.153 482 Planarity : 0.004 0.030 504 Dihedral : 5.925 57.015 431 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.52 % Allowed : 18.79 % Favored : 79.70 % 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: 2.31 (0.46), residues: 360 helix: 2.58 (0.33), residues: 245 sheet: 1.74 (1.14), residues: 22 loop : -1.58 (0.63), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 133 HIS 0.002 0.000 HIS B 73 PHE 0.013 0.001 PHE A 141 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 54 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.339 Fit side-chains REVERT: A 15 LYS cc_start: 0.6504 (mmtm) cc_final: 0.6273 (mmpt) REVERT: A 216 ARG cc_start: 0.8302 (mtm180) cc_final: 0.7954 (ptp-110) REVERT: B 216 ARG cc_start: 0.8284 (tpm-80) cc_final: 0.7573 (tpt90) outliers start: 5 outliers final: 4 residues processed: 53 average time/residue: 1.2922 time to fit residues: 70.2859 Evaluate side-chains 50 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 212 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 22 optimal weight: 0.0770 chunk 4 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 21 optimal weight: 0.0370 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- 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 = 0.3492 r_free = 0.3492 target = 0.082808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.059954 restraints weight = 8368.686| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.50 r_work: 0.2816 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 3132 Z= 0.181 Angle : 0.620 8.896 4240 Z= 0.318 Chirality : 0.040 0.142 482 Planarity : 0.003 0.031 504 Dihedral : 5.394 51.077 431 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.91 % Allowed : 20.30 % 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: 2.42 (0.46), residues: 360 helix: 2.66 (0.33), residues: 245 sheet: 1.89 (1.17), residues: 22 loop : -1.55 (0.62), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 133 HIS 0.002 0.000 HIS B 16 PHE 0.046 0.001 PHE B 29 TYR 0.006 0.001 TYR B 97 ARG 0.004 0.000 ARG B 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2653.01 seconds wall clock time: 47 minutes 26.25 seconds (2846.25 seconds total)