Starting phenix.real_space_refine on Wed Mar 5 21:09:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qev_13942/03_2025/7qev_13942.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qev_13942/03_2025/7qev_13942.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/7qev_13942/03_2025/7qev_13942.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qev_13942/03_2025/7qev_13942.map" model { file = "/net/cci-nas-00/data/ceres_data/7qev_13942/03_2025/7qev_13942.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qev_13942/03_2025/7qev_13942.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 30 5.16 5 C 2141 2.51 5 N 504 2.21 5 O 529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3204 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1577 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 186} Chain breaks: 1 Chain: "B" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1548 Classifications: {'peptide': 190} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 183} Chain breaks: 1 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 37 Unusual residues: {'LMT': 3, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {'LMT': 3, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 2.75, per 1000 atoms: 0.86 Number of scatterers: 3204 At special positions: 0 Unit cell: (71.94, 64.31, 92.65, 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 30 16.00 O 529 8.00 N 504 7.00 C 2141 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: 0.78 Conformation dependent library (CDL) restraints added in 338.2 milliseconds 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 730 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 2 sheets defined 75.5% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 removed outlier: 4.411A pdb=" N LYS A 15 " --> pdb=" O GLY A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 39 removed outlier: 3.548A pdb=" N ILE A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N THR A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 43 Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 72 through 95 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.959A pdb=" N LYS A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 159 removed outlier: 3.816A pdb=" N TRP A 134 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 145 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 155 " --> pdb=" O MET A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 216 removed outlier: 3.614A pdb=" N GLU A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 210 " --> pdb=" O ASN A 206 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG A 216 " --> pdb=" O TYR A 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 15 removed outlier: 3.855A pdb=" N LYS B 15 " --> pdb=" O GLY B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 39 removed outlier: 4.263A pdb=" N LEU B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 47 removed outlier: 4.084A pdb=" N TRP B 44 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY B 45 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASP B 46 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B 47 " --> pdb=" O TRP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 72 through 84 Processing helix chain 'B' and resid 85 through 101 removed outlier: 3.564A pdb=" N VAL B 91 " --> pdb=" O PRO B 87 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU B 101 " --> pdb=" O TYR B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 159 removed outlier: 3.585A pdb=" N ILE B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 145 " --> pdb=" O PHE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 217 removed outlier: 4.012A pdb=" N ARG B 216 " --> pdb=" O TYR B 212 " (cutoff:3.500A) 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 53 210 hydrogen bonds defined for protein. 612 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: 0.75 Time building geometry restraints manager: 0.94 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: 927 1.34 - 1.46: 689 1.46 - 1.57: 1618 1.57 - 1.69: 0 1.69 - 1.80: 44 Bond restraints: 3278 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 5.94e+00 bond pdb=" C1 LMT B 302 " pdb=" C2 LMT B 302 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.00e-02 2.50e+03 5.83e+00 bond pdb=" C7 LMT A 303 " pdb=" C8 LMT A 303 " ideal model delta sigma weight residual 1.529 1.568 -0.039 2.00e-02 2.50e+03 3.90e+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 3.60e+00 bond pdb=" C7 LMT B 302 " pdb=" C8 LMT B 302 " ideal model delta sigma weight residual 1.529 1.566 -0.037 2.00e-02 2.50e+03 3.42e+00 ... (remaining 3273 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 4248 1.63 - 3.27: 114 3.27 - 4.90: 32 4.90 - 6.53: 26 6.53 - 8.16: 9 Bond angle restraints: 4429 Sorted by residual: angle pdb=" C6 LMT A 303 " pdb=" C7 LMT A 303 " pdb=" C8 LMT A 303 " ideal model delta sigma weight residual 117.26 109.10 8.16 3.00e+00 1.11e-01 7.41e+00 angle pdb=" C6 LMT A 301 " pdb=" C7 LMT A 301 " pdb=" C8 LMT A 301 " ideal model delta sigma weight residual 117.26 109.62 7.64 3.00e+00 1.11e-01 6.48e+00 angle pdb=" C6 LMT A 302 " pdb=" C7 LMT A 302 " pdb=" C8 LMT A 302 " ideal model delta sigma weight residual 117.26 109.64 7.62 3.00e+00 1.11e-01 6.45e+00 angle pdb=" C2 LMT A 301 " pdb=" C3 LMT A 301 " pdb=" C4 LMT A 301 " ideal model delta sigma weight residual 117.09 109.67 7.42 3.00e+00 1.11e-01 6.12e+00 angle pdb=" C6 LMT B 302 " pdb=" C7 LMT B 302 " pdb=" C8 LMT B 302 " ideal model delta sigma weight residual 117.26 110.14 7.12 3.00e+00 1.11e-01 5.64e+00 ... (remaining 4424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 1707 17.88 - 35.76: 164 35.76 - 53.64: 24 53.64 - 71.52: 3 71.52 - 89.40: 1 Dihedral angle restraints: 1899 sinusoidal: 772 harmonic: 1127 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 -157.45 -22.55 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA ILE B 23 " pdb=" C ILE B 23 " pdb=" N TRP B 24 " pdb=" CA TRP B 24 " ideal model delta harmonic sigma weight residual -180.00 -158.55 -21.45 0 5.00e+00 4.00e-02 1.84e+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 -159.14 -20.86 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 1896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 209 0.029 - 0.058: 203 0.058 - 0.088: 58 0.088 - 0.117: 20 0.117 - 0.146: 7 Chirality restraints: 497 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 2.38 0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CA PRO B 185 " pdb=" N PRO B 185 " pdb=" C PRO B 185 " pdb=" CB PRO B 185 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.59e-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 2.40 0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 494 not shown) Planarity restraints: 526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 174 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO A 175 " -0.051 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=" CB ASN A 176 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.34e+00 pdb=" CG ASN A 176 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 176 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 176 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 86 " 0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO A 87 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 87 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 87 " 0.015 5.00e-02 4.00e+02 ... (remaining 523 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 124 2.71 - 3.26: 3328 3.26 - 3.81: 4894 3.81 - 4.35: 5842 4.35 - 4.90: 9936 Nonbonded interactions: 24124 Sorted by model distance: nonbonded pdb=" O ILE B 71 " pdb=" OH TYR B 158 " model vdw 2.164 3.040 nonbonded pdb=" O ILE A 71 " pdb=" OH TYR A 158 " model vdw 2.167 3.040 nonbonded pdb=" O TYR B 152 " pdb=" O HOH B 401 " model vdw 2.211 3.040 nonbonded pdb=" O SER A 17 " pdb=" NZ LYS A 22 " model vdw 2.260 3.120 nonbonded pdb=" OH TYR B 68 " pdb=" O LYS B 168 " model vdw 2.284 3.040 ... (remaining 24119 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 1 through 101 or resid 129 through 217 or (resid 301 and ( \ name C4 or name C5 or name C6 or name C7 )) or resid 302 through 304)) selection = (chain 'B' and (resid 1 through 217 or resid 301 or (resid 302 and (name C2 or n \ ame C3 or name C4 or name C5 or name C6 or name C7 or name C8 )) or resid 303 th \ rough 304)) } 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: 0.260 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: 0.020 Set scattering table: 0.030 Process input model: 12.170 Find NCS groups from input model: 0.120 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:11.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 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 : 0.009 0.054 3278 Z= 0.578 Angle : 0.863 8.164 4429 Z= 0.404 Chirality : 0.046 0.146 497 Planarity : 0.003 0.029 526 Dihedral : 13.679 89.401 1151 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % 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: -0.15 (0.42), residues: 375 helix: 0.22 (0.31), residues: 247 sheet: 0.19 (0.90), residues: 34 loop : -0.70 (0.66), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 24 HIS 0.002 0.001 HIS A 73 PHE 0.012 0.002 PHE A 31 TYR 0.012 0.002 TYR B 65 ARG 0.003 0.001 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: B 41 LYS cc_start: 0.9261 (tttt) cc_final: 0.9016 (tttt) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 1.2871 time to fit residues: 79.3240 Evaluate side-chains 46 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3506 r_free = 0.3506 target = 0.082393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.058115 restraints weight = 8926.374| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.56 r_work: 0.2738 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3278 Z= 0.233 Angle : 0.680 8.492 4429 Z= 0.367 Chirality : 0.042 0.135 497 Planarity : 0.004 0.027 526 Dihedral : 7.224 58.588 455 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.46 % Allowed : 10.20 % Favored : 88.34 % 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: 1.26 (0.43), residues: 375 helix: 1.58 (0.32), residues: 251 sheet: 0.69 (1.01), residues: 28 loop : -1.09 (0.64), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 133 HIS 0.003 0.001 HIS B 94 PHE 0.021 0.002 PHE A 29 TYR 0.012 0.002 TYR B 65 ARG 0.003 0.001 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.327 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 57 average time/residue: 1.0858 time to fit residues: 63.8340 Evaluate side-chains 47 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 211 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 20 optimal weight: 30.0000 chunk 34 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.084494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.060078 restraints weight = 8780.936| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.55 r_work: 0.2793 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3278 Z= 0.181 Angle : 0.586 7.349 4429 Z= 0.311 Chirality : 0.041 0.139 497 Planarity : 0.003 0.024 526 Dihedral : 5.888 52.827 455 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.92 % Allowed : 13.99 % Favored : 83.09 % 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: 1.77 (0.43), residues: 375 helix: 2.06 (0.33), residues: 251 sheet: 1.42 (1.11), residues: 22 loop : -1.19 (0.57), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 134 HIS 0.003 0.001 HIS B 16 PHE 0.027 0.001 PHE A 29 TYR 0.008 0.001 TYR B 152 ARG 0.004 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.8181 (m-10) outliers start: 10 outliers final: 2 residues processed: 63 average time/residue: 1.1191 time to fit residues: 72.6751 Evaluate side-chains 54 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 97 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 30.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.083911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.059811 restraints weight = 8907.266| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.51 r_work: 0.2782 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3278 Z= 0.215 Angle : 0.626 8.579 4429 Z= 0.320 Chirality : 0.042 0.164 497 Planarity : 0.003 0.026 526 Dihedral : 5.578 49.054 455 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.17 % Allowed : 18.66 % Favored : 80.17 % 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: 1.91 (0.44), residues: 375 helix: 2.17 (0.33), residues: 253 sheet: 1.41 (1.11), residues: 22 loop : -1.20 (0.59), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 133 HIS 0.001 0.001 HIS A 73 PHE 0.022 0.001 PHE A 29 TYR 0.008 0.001 TYR B 65 ARG 0.004 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8767 (mttp) cc_final: 0.8244 (mttp) REVERT: A 141 PHE cc_start: 0.8659 (t80) cc_final: 0.8426 (t80) REVERT: A 212 TYR cc_start: 0.8574 (OUTLIER) cc_final: 0.8135 (m-10) outliers start: 4 outliers final: 1 residues processed: 55 average time/residue: 1.2195 time to fit residues: 69.0438 Evaluate side-chains 53 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 97 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.082682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.058446 restraints weight = 9000.142| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.51 r_work: 0.2751 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 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 : 0.004 0.034 3278 Z= 0.266 Angle : 0.616 8.139 4429 Z= 0.322 Chirality : 0.043 0.159 497 Planarity : 0.004 0.028 526 Dihedral : 5.501 44.487 455 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.33 % Allowed : 18.37 % Favored : 79.30 % 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: 2.01 (0.44), residues: 375 helix: 2.27 (0.33), residues: 251 sheet: 1.26 (1.10), residues: 22 loop : -1.10 (0.60), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 44 HIS 0.002 0.001 HIS A 73 PHE 0.011 0.001 PHE A 31 TYR 0.011 0.001 TYR B 65 ARG 0.004 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 PHE cc_start: 0.8779 (t80) cc_final: 0.8539 (t80) REVERT: A 212 TYR cc_start: 0.8689 (OUTLIER) cc_final: 0.8223 (m-10) outliers start: 8 outliers final: 4 residues processed: 59 average time/residue: 1.0535 time to fit residues: 64.1595 Evaluate side-chains 54 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 211 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 14 optimal weight: 0.0970 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 0.1980 chunk 31 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.083585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.059317 restraints weight = 9164.053| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.58 r_work: 0.2769 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3278 Z= 0.211 Angle : 0.616 8.496 4429 Z= 0.315 Chirality : 0.042 0.158 497 Planarity : 0.003 0.028 526 Dihedral : 5.196 39.731 455 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.75 % Allowed : 20.41 % Favored : 77.84 % 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: 2.01 (0.44), residues: 375 helix: 2.30 (0.32), residues: 252 sheet: 1.34 (1.10), residues: 22 loop : -1.29 (0.60), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 24 HIS 0.001 0.001 HIS B 73 PHE 0.025 0.001 PHE A 29 TYR 0.009 0.001 TYR A 97 ARG 0.002 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7864 (ppp) REVERT: A 141 PHE cc_start: 0.8648 (t80) cc_final: 0.8416 (t80) REVERT: A 212 TYR cc_start: 0.8583 (OUTLIER) cc_final: 0.8108 (m-10) outliers start: 6 outliers final: 2 residues processed: 56 average time/residue: 1.1696 time to fit residues: 67.4944 Evaluate side-chains 56 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 97 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 0.3980 chunk 3 optimal weight: 0.4980 chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 34 optimal weight: 0.0030 chunk 13 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.085064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.061070 restraints weight = 8905.500| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.57 r_work: 0.2818 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3278 Z= 0.163 Angle : 0.585 8.235 4429 Z= 0.295 Chirality : 0.041 0.156 497 Planarity : 0.003 0.028 526 Dihedral : 4.677 31.371 455 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.62 % Allowed : 20.41 % Favored : 76.97 % 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: 2.08 (0.44), residues: 375 helix: 2.38 (0.32), residues: 253 sheet: 1.44 (1.11), residues: 22 loop : -1.41 (0.58), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 133 HIS 0.002 0.000 HIS A 73 PHE 0.008 0.001 PHE A 31 TYR 0.010 0.001 TYR A 97 ARG 0.003 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.7857 (ppp) REVERT: A 212 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.8101 (m-10) REVERT: B 1 MET cc_start: 0.4631 (mmm) cc_final: 0.2902 (mpp) outliers start: 9 outliers final: 2 residues processed: 61 average time/residue: 1.1386 time to fit residues: 72.0052 Evaluate side-chains 57 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 97 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 31 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3550 r_free = 0.3550 target = 0.084735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.060936 restraints weight = 8805.512| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.51 r_work: 0.2814 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3278 Z= 0.197 Angle : 0.629 10.089 4429 Z= 0.315 Chirality : 0.042 0.160 497 Planarity : 0.003 0.028 526 Dihedral : 4.625 27.038 455 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.04 % Allowed : 22.16 % Favored : 75.80 % 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: 2.00 (0.44), residues: 375 helix: 2.31 (0.32), residues: 254 sheet: 1.47 (1.10), residues: 22 loop : -1.43 (0.58), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 44 HIS 0.002 0.000 HIS A 73 PHE 0.018 0.001 PHE A 141 TYR 0.009 0.001 TYR A 97 ARG 0.002 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 93 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.7828 (ppp) REVERT: A 212 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.8128 (m-10) REVERT: B 1 MET cc_start: 0.4425 (mmm) cc_final: 0.3192 (mpp) REVERT: B 41 LYS cc_start: 0.9113 (tttt) cc_final: 0.8646 (tmmt) outliers start: 7 outliers final: 4 residues processed: 58 average time/residue: 1.0988 time to fit residues: 65.6875 Evaluate side-chains 57 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 211 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 0.1980 chunk 34 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.085318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.061474 restraints weight = 8932.899| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.57 r_work: 0.2830 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3278 Z= 0.169 Angle : 0.636 10.351 4429 Z= 0.314 Chirality : 0.043 0.153 497 Planarity : 0.003 0.028 526 Dihedral : 4.430 22.788 455 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.46 % Allowed : 23.91 % Favored : 74.64 % 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: 2.00 (0.43), residues: 375 helix: 2.32 (0.32), residues: 254 sheet: 1.51 (1.11), residues: 22 loop : -1.47 (0.58), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 133 HIS 0.002 0.001 HIS A 73 PHE 0.016 0.001 PHE A 141 TYR 0.010 0.001 TYR A 97 ARG 0.001 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 29 PHE cc_start: 0.9036 (t80) cc_final: 0.8792 (t80) REVERT: A 93 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.7724 (tmm) REVERT: B 1 MET cc_start: 0.4412 (mmm) cc_final: 0.3213 (mpp) REVERT: B 41 LYS cc_start: 0.9105 (tttt) cc_final: 0.8619 (tmmt) REVERT: B 50 ASP cc_start: 0.8762 (m-30) cc_final: 0.8505 (m-30) outliers start: 5 outliers final: 2 residues processed: 60 average time/residue: 1.1728 time to fit residues: 72.3937 Evaluate side-chains 52 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain B residue 97 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 29 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 16 optimal weight: 0.0870 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.085325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.061354 restraints weight = 8814.837| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.59 r_work: 0.2832 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3278 Z= 0.187 Angle : 0.680 10.719 4429 Z= 0.334 Chirality : 0.045 0.312 497 Planarity : 0.003 0.028 526 Dihedral : 4.310 20.390 455 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.87 % Allowed : 25.66 % Favored : 73.47 % 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: 2.04 (0.44), residues: 375 helix: 2.33 (0.32), residues: 254 sheet: 1.54 (1.11), residues: 22 loop : -1.42 (0.60), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 44 HIS 0.002 0.000 HIS A 73 PHE 0.017 0.001 PHE A 141 TYR 0.010 0.001 TYR A 97 ARG 0.003 0.000 ARG A 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 29 PHE cc_start: 0.9046 (t80) cc_final: 0.8787 (t80) REVERT: A 93 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7663 (tmm) REVERT: B 1 MET cc_start: 0.4388 (mmm) cc_final: 0.3207 (mpp) REVERT: B 41 LYS cc_start: 0.9088 (tttt) cc_final: 0.8589 (tmmt) REVERT: B 50 ASP cc_start: 0.8763 (m-30) cc_final: 0.8496 (m-30) outliers start: 3 outliers final: 2 residues processed: 54 average time/residue: 1.0629 time to fit residues: 59.2829 Evaluate side-chains 53 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain B residue 97 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 4 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 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 = 0.3555 r_free = 0.3555 target = 0.085477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.061751 restraints weight = 8813.612| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.53 r_work: 0.2834 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3278 Z= 0.192 Angle : 0.676 11.901 4429 Z= 0.331 Chirality : 0.043 0.170 497 Planarity : 0.003 0.028 526 Dihedral : 4.332 18.906 455 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.17 % Allowed : 25.66 % Favored : 73.18 % 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: 2.03 (0.44), residues: 375 helix: 2.31 (0.32), residues: 254 sheet: 1.55 (1.11), residues: 22 loop : -1.39 (0.60), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 44 HIS 0.001 0.000 HIS B 73 PHE 0.016 0.001 PHE A 141 TYR 0.010 0.001 TYR A 97 ARG 0.002 0.000 ARG A 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2477.55 seconds wall clock time: 43 minutes 7.20 seconds (2587.20 seconds total)