Starting phenix.real_space_refine on Wed Sep 17 03:31:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zpn_60350/09_2025/8zpn_60350.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zpn_60350/09_2025/8zpn_60350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zpn_60350/09_2025/8zpn_60350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zpn_60350/09_2025/8zpn_60350.map" model { file = "/net/cci-nas-00/data/ceres_data/8zpn_60350/09_2025/8zpn_60350.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zpn_60350/09_2025/8zpn_60350.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 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 15 5.16 5 C 2116 2.51 5 N 527 2.21 5 O 546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3204 Number of models: 1 Model: "" Number of chains: 3 Chain: "R" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2292 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 10, 'TRANS': 271} Chain: "N" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 848 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'CLR': 1, 'VH6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 0.92, per 1000 atoms: 0.29 Number of scatterers: 3204 At special positions: 0 Unit cell: (73.95, 53.55, 120.7, 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 15 16.00 O 546 8.00 N 527 7.00 C 2116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS N 24 " - pdb=" SG CYS N 97 " 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: 0.31 Conformation dependent library (CDL) restraints added in 122.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 5 sheets defined 61.1% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'R' and resid 34 through 65 Proline residue: R 42 - end of helix Processing helix chain 'R' and resid 71 through 100 Proline residue: R 92 - end of helix Processing helix chain 'R' and resid 105 through 140 removed outlier: 3.647A pdb=" N TRP R 125 " --> pdb=" O TYR R 121 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA R 128 " --> pdb=" O VAL R 124 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS R 140 " --> pdb=" O LEU R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 154 removed outlier: 5.177A pdb=" N LEU R 151 " --> pdb=" O PRO R 147 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA R 152 " --> pdb=" O ARG R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 167 removed outlier: 4.365A pdb=" N ILE R 162 " --> pdb=" O VAL R 158 " (cutoff:3.500A) Proline residue: R 163 - end of helix Processing helix chain 'R' and resid 168 through 174 Processing helix chain 'R' and resid 192 through 227 removed outlier: 3.562A pdb=" N VAL R 196 " --> pdb=" O ASN R 192 " (cutoff:3.500A) Proline residue: R 211 - end of helix Processing helix chain 'R' and resid 235 through 275 Proline residue: R 248 - end of helix Proline residue: R 262 - end of helix Processing helix chain 'R' and resid 281 through 300 removed outlier: 4.045A pdb=" N GLU R 285 " --> pdb=" O GLY R 281 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN R 286 " --> pdb=" O CYS R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 303 No H-bonds generated for 'chain 'R' and resid 301 through 303' Processing helix chain 'R' and resid 304 through 313 removed outlier: 3.747A pdb=" N ILE R 308 " --> pdb=" O CYS R 304 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 92 Processing sheet with id=AA1, first strand: chain 'R' and resid 175 through 177 removed outlier: 3.600A pdb=" N ASP R 187 " --> pdb=" O ASN R 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AA3, first strand: chain 'N' and resid 12 through 14 removed outlier: 3.906A pdb=" N THR N 120 " --> pdb=" O GLY N 12 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL N 14 " --> pdb=" O THR N 120 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP N 35 " --> pdb=" O GLU N 100 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ARG N 102 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU N 33 " --> pdb=" O ARG N 102 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N TYR N 34 " --> pdb=" O THR N 54 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N THR N 54 " --> pdb=" O TYR N 34 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N MET N 36 " --> pdb=" O SER N 52 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER N 52 " --> pdb=" O MET N 36 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TRP N 38 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL N 50 " --> pdb=" O TRP N 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 12 through 14 removed outlier: 3.906A pdb=" N THR N 120 " --> pdb=" O GLY N 12 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL N 14 " --> pdb=" O THR N 120 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 21 through 22 removed outlier: 3.533A pdb=" N LEU N 82 " --> pdb=" O LEU N 22 " (cutoff:3.500A) 200 hydrogen bonds defined for protein. 564 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: 0.28 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 975 1.34 - 1.46: 836 1.46 - 1.58: 1455 1.58 - 1.70: 0 1.70 - 1.82: 20 Bond restraints: 3286 Sorted by residual: bond pdb=" C05 VH6 R 402 " pdb=" C06 VH6 R 402 " ideal model delta sigma weight residual 1.543 1.501 0.042 2.00e-02 2.50e+03 4.39e+00 bond pdb=" C06 VH6 R 402 " pdb=" C07 VH6 R 402 " ideal model delta sigma weight residual 1.542 1.501 0.041 2.00e-02 2.50e+03 4.12e+00 bond pdb=" C09 VH6 R 402 " pdb=" C10 VH6 R 402 " ideal model delta sigma weight residual 1.530 1.493 0.037 2.00e-02 2.50e+03 3.38e+00 bond pdb=" C12 VH6 R 402 " pdb=" C13 VH6 R 402 " ideal model delta sigma weight residual 1.537 1.501 0.036 2.00e-02 2.50e+03 3.18e+00 bond pdb=" C02 VH6 R 402 " pdb=" C03 VH6 R 402 " ideal model delta sigma weight residual 1.527 1.496 0.031 2.00e-02 2.50e+03 2.40e+00 ... (remaining 3281 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 4309 1.27 - 2.55: 120 2.55 - 3.82: 25 3.82 - 5.09: 10 5.09 - 6.37: 9 Bond angle restraints: 4473 Sorted by residual: angle pdb=" C PHE R 201 " pdb=" N GLN R 202 " pdb=" CA GLN R 202 " ideal model delta sigma weight residual 120.31 117.03 3.28 1.52e+00 4.33e-01 4.65e+00 angle pdb=" C06 VH6 R 402 " pdb=" C05 VH6 R 402 " pdb=" N04 VH6 R 402 " ideal model delta sigma weight residual 117.45 111.08 6.37 3.00e+00 1.11e-01 4.50e+00 angle pdb=" N LEU R 91 " pdb=" CA LEU R 91 " pdb=" C LEU R 91 " ideal model delta sigma weight residual 113.16 116.15 -2.99 1.42e+00 4.96e-01 4.45e+00 angle pdb=" C13 VH6 R 402 " pdb=" C12 VH6 R 402 " pdb=" N11 VH6 R 402 " ideal model delta sigma weight residual 117.46 111.23 6.23 3.00e+00 1.11e-01 4.31e+00 angle pdb=" C16 VH6 R 402 " pdb=" C15 VH6 R 402 " pdb=" N08 VH6 R 402 " ideal model delta sigma weight residual 115.75 121.85 -6.10 3.00e+00 1.11e-01 4.13e+00 ... (remaining 4468 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.26: 1901 33.26 - 66.51: 48 66.51 - 99.77: 6 99.77 - 133.02: 8 133.02 - 166.28: 5 Dihedral angle restraints: 1968 sinusoidal: 808 harmonic: 1160 Sorted by residual: dihedral pdb=" C31 VH6 R 402 " pdb=" C32 VH6 R 402 " pdb=" C33 VH6 R 402 " pdb=" N34 VH6 R 402 " ideal model delta sinusoidal sigma weight residual -72.66 93.62 -166.28 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C05 VH6 R 402 " pdb=" C06 VH6 R 402 " pdb=" C07 VH6 R 402 " pdb=" N08 VH6 R 402 " ideal model delta sinusoidal sigma weight residual 118.54 -46.85 165.39 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C09 VH6 R 402 " pdb=" C10 VH6 R 402 " pdb=" N11 VH6 R 402 " pdb=" C12 VH6 R 402 " ideal model delta sinusoidal sigma weight residual -131.28 28.15 -159.43 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 1965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 283 0.025 - 0.051: 128 0.051 - 0.076: 62 0.076 - 0.101: 24 0.101 - 0.126: 17 Chirality restraints: 514 Sorted by residual: chirality pdb=" CB ILE N 53 " pdb=" CA ILE N 53 " pdb=" CG1 ILE N 53 " pdb=" CG2 ILE N 53 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 4.00e-01 chirality pdb=" CA ILE R 278 " pdb=" N ILE R 278 " pdb=" C ILE R 278 " pdb=" CB ILE R 278 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.38e-01 chirality pdb=" CA ARG R 247 " pdb=" N ARG R 247 " pdb=" C ARG R 247 " pdb=" CB ARG R 247 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.34e-01 ... (remaining 511 not shown) Planarity restraints: 541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 206 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C VAL R 206 " 0.044 2.00e-02 2.50e+03 pdb=" O VAL R 206 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY R 207 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG R 146 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO R 147 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO R 147 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 147 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG R 247 " 0.035 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO R 248 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO R 248 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO R 248 " 0.030 5.00e-02 4.00e+02 ... (remaining 538 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1040 2.84 - 3.35: 3030 3.35 - 3.87: 5086 3.87 - 4.38: 5745 4.38 - 4.90: 10156 Nonbonded interactions: 25057 Sorted by model distance: nonbonded pdb=" OE2 GLU R 283 " pdb=" OG1 THR R 287 " model vdw 2.323 3.040 nonbonded pdb=" OD1 ASP R 270 " pdb=" N01 VH6 R 402 " model vdw 2.333 3.120 nonbonded pdb=" OD1 ASN R 101 " pdb=" N TYR R 184 " model vdw 2.339 3.120 nonbonded pdb=" NZ LYS R 110 " pdb=" O ALA R 175 " model vdw 2.344 3.120 nonbonded pdb=" O LEU R 242 " pdb=" OG1 THR R 246 " model vdw 2.346 3.040 ... (remaining 25052 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 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: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.320 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3288 Z= 0.174 Angle : 0.602 6.365 4477 Z= 0.302 Chirality : 0.041 0.126 514 Planarity : 0.005 0.055 541 Dihedral : 20.015 166.280 1218 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.43), residues: 392 helix: 1.21 (0.34), residues: 222 sheet: 0.20 (0.92), residues: 37 loop : -1.49 (0.53), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 77 TYR 0.011 0.001 TYR R 219 PHE 0.009 0.001 PHE R 256 TRP 0.005 0.001 TRP R 195 HIS 0.004 0.001 HIS R 203 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 3286) covalent geometry : angle 0.60219 ( 4473) SS BOND : bond 0.00144 ( 2) SS BOND : angle 0.48055 ( 4) hydrogen bonds : bond 0.14704 ( 195) hydrogen bonds : angle 6.21818 ( 564) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.085 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0734 time to fit residues: 4.1493 Evaluate side-chains 40 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4167 r_free = 0.4167 target = 0.192216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.148179 restraints weight = 3614.553| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.38 r_work: 0.3565 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3288 Z= 0.153 Angle : 0.557 5.640 4477 Z= 0.294 Chirality : 0.042 0.120 514 Planarity : 0.005 0.048 541 Dihedral : 21.074 174.820 542 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.74 % Allowed : 7.01 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.42), residues: 392 helix: 1.16 (0.34), residues: 228 sheet: 0.48 (0.82), residues: 37 loop : -1.38 (0.54), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 68 TYR 0.015 0.001 TYR R 219 PHE 0.013 0.001 PHE N 69 TRP 0.008 0.001 TRP N 113 HIS 0.002 0.001 HIS R 203 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 3286) covalent geometry : angle 0.55748 ( 4473) SS BOND : bond 0.00158 ( 2) SS BOND : angle 0.31637 ( 4) hydrogen bonds : bond 0.06262 ( 195) hydrogen bonds : angle 4.93728 ( 564) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.118 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 44 average time/residue: 0.0648 time to fit residues: 3.5494 Evaluate side-chains 46 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 200 GLN Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 103 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.186194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.142969 restraints weight = 3562.248| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.27 r_work: 0.3520 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3288 Z= 0.170 Angle : 0.567 5.636 4477 Z= 0.299 Chirality : 0.042 0.121 514 Planarity : 0.005 0.045 541 Dihedral : 18.507 173.613 542 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.44 % Allowed : 12.20 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.42), residues: 392 helix: 1.10 (0.33), residues: 227 sheet: 0.52 (0.85), residues: 37 loop : -1.46 (0.55), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 243 TYR 0.015 0.001 TYR R 219 PHE 0.011 0.001 PHE R 256 TRP 0.007 0.001 TRP N 113 HIS 0.002 0.001 HIS R 203 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 3286) covalent geometry : angle 0.56697 ( 4473) SS BOND : bond 0.00146 ( 2) SS BOND : angle 0.44994 ( 4) hydrogen bonds : bond 0.06523 ( 195) hydrogen bonds : angle 4.93187 ( 564) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.091 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 42 average time/residue: 0.0588 time to fit residues: 3.0914 Evaluate side-chains 43 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 200 GLN Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain N residue 103 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 10 optimal weight: 0.0670 chunk 3 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.188628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.145407 restraints weight = 3549.961| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.28 r_work: 0.3550 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3288 Z= 0.140 Angle : 0.520 5.522 4477 Z= 0.275 Chirality : 0.041 0.118 514 Planarity : 0.004 0.042 541 Dihedral : 17.185 171.247 542 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.13 % Allowed : 14.02 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.43), residues: 392 helix: 1.32 (0.34), residues: 228 sheet: 0.47 (0.86), residues: 37 loop : -1.36 (0.57), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 68 TYR 0.013 0.001 TYR R 219 PHE 0.009 0.001 PHE R 256 TRP 0.005 0.001 TRP N 106 HIS 0.002 0.001 HIS R 203 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 3286) covalent geometry : angle 0.52041 ( 4473) SS BOND : bond 0.00267 ( 2) SS BOND : angle 0.58895 ( 4) hydrogen bonds : bond 0.05853 ( 195) hydrogen bonds : angle 4.74470 ( 564) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.118 Fit side-chains revert: symmetry clash REVERT: R 200 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7479 (tt0) REVERT: N 84 MET cc_start: 0.6224 (mmm) cc_final: 0.5882 (mmt) outliers start: 7 outliers final: 6 residues processed: 42 average time/residue: 0.0624 time to fit residues: 3.3007 Evaluate side-chains 44 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 200 GLN Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain N residue 79 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 34 optimal weight: 9.9990 chunk 6 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 9 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 0.2980 chunk 10 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4128 r_free = 0.4128 target = 0.189458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.146127 restraints weight = 3523.525| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.32 r_work: 0.3560 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3288 Z= 0.135 Angle : 0.505 5.560 4477 Z= 0.267 Chirality : 0.040 0.117 514 Planarity : 0.004 0.041 541 Dihedral : 15.513 133.383 542 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.05 % Allowed : 14.33 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.43), residues: 392 helix: 1.41 (0.34), residues: 228 sheet: 0.47 (0.83), residues: 37 loop : -1.33 (0.57), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 73 TYR 0.012 0.001 TYR R 219 PHE 0.009 0.001 PHE R 256 TRP 0.006 0.001 TRP R 195 HIS 0.002 0.001 HIS R 203 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 3286) covalent geometry : angle 0.50487 ( 4473) SS BOND : bond 0.00044 ( 2) SS BOND : angle 0.43577 ( 4) hydrogen bonds : bond 0.05657 ( 195) hydrogen bonds : angle 4.63239 ( 564) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.102 Fit side-chains REVERT: R 200 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7273 (tt0) outliers start: 10 outliers final: 6 residues processed: 44 average time/residue: 0.0554 time to fit residues: 3.0882 Evaluate side-chains 43 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 200 GLN Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain N residue 103 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 16 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 33 optimal weight: 0.3980 chunk 30 optimal weight: 7.9990 chunk 12 optimal weight: 0.0070 chunk 17 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.189722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.146517 restraints weight = 3529.079| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.33 r_work: 0.3569 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3288 Z= 0.135 Angle : 0.515 5.576 4477 Z= 0.272 Chirality : 0.041 0.118 514 Planarity : 0.004 0.042 541 Dihedral : 14.541 128.045 542 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.13 % Allowed : 15.85 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.43), residues: 392 helix: 1.41 (0.34), residues: 228 sheet: 0.24 (0.83), residues: 37 loop : -1.28 (0.57), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 188 TYR 0.013 0.001 TYR R 219 PHE 0.009 0.001 PHE R 256 TRP 0.006 0.001 TRP R 195 HIS 0.002 0.001 HIS R 302 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 3286) covalent geometry : angle 0.51531 ( 4473) SS BOND : bond 0.00151 ( 2) SS BOND : angle 0.41757 ( 4) hydrogen bonds : bond 0.05647 ( 195) hydrogen bonds : angle 4.63716 ( 564) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.135 Fit side-chains REVERT: R 200 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7287 (tt0) outliers start: 7 outliers final: 6 residues processed: 39 average time/residue: 0.0536 time to fit residues: 2.7533 Evaluate side-chains 43 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 200 GLN Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain N residue 103 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.0040 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 12 optimal weight: 0.0170 chunk 38 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 overall best weight: 0.3630 ------------------------------------------------------------------------------- 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 = 0.4150 r_free = 0.4150 target = 0.191801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.148382 restraints weight = 3572.795| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.36 r_work: 0.3584 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3288 Z= 0.123 Angle : 0.508 6.877 4477 Z= 0.264 Chirality : 0.040 0.116 514 Planarity : 0.005 0.076 541 Dihedral : 13.720 127.020 542 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.13 % Allowed : 17.07 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.43), residues: 392 helix: 1.54 (0.34), residues: 228 sheet: 0.14 (0.82), residues: 37 loop : -1.23 (0.57), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 188 TYR 0.011 0.001 TYR R 219 PHE 0.008 0.001 PHE R 256 TRP 0.006 0.001 TRP R 195 HIS 0.002 0.001 HIS R 302 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 3286) covalent geometry : angle 0.50806 ( 4473) SS BOND : bond 0.00137 ( 2) SS BOND : angle 0.36791 ( 4) hydrogen bonds : bond 0.05333 ( 195) hydrogen bonds : angle 4.54167 ( 564) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.127 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 39 average time/residue: 0.0572 time to fit residues: 2.9349 Evaluate side-chains 43 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain N residue 36 MET Chi-restraints excluded: chain N residue 103 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.186614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.142154 restraints weight = 3639.167| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.36 r_work: 0.3493 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3288 Z= 0.201 Angle : 0.601 8.342 4477 Z= 0.314 Chirality : 0.044 0.125 514 Planarity : 0.005 0.059 541 Dihedral : 13.844 128.302 542 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.74 % Allowed : 16.46 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.42), residues: 392 helix: 1.01 (0.33), residues: 227 sheet: 0.42 (0.88), residues: 37 loop : -1.40 (0.56), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 188 TYR 0.019 0.001 TYR R 219 PHE 0.013 0.001 PHE R 256 TRP 0.010 0.001 TRP R 291 HIS 0.001 0.001 HIS R 203 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 3286) covalent geometry : angle 0.60141 ( 4473) SS BOND : bond 0.00098 ( 2) SS BOND : angle 0.60920 ( 4) hydrogen bonds : bond 0.06802 ( 195) hydrogen bonds : angle 4.89021 ( 564) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.124 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 43 average time/residue: 0.0516 time to fit residues: 2.9210 Evaluate side-chains 45 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 200 GLN Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain N residue 36 MET Chi-restraints excluded: chain N residue 103 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.189010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.145169 restraints weight = 3639.085| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.34 r_work: 0.3527 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3288 Z= 0.148 Angle : 0.558 9.371 4477 Z= 0.289 Chirality : 0.041 0.117 514 Planarity : 0.004 0.039 541 Dihedral : 13.714 128.132 542 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.05 % Allowed : 16.77 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.43), residues: 392 helix: 1.18 (0.34), residues: 229 sheet: 0.28 (0.86), residues: 37 loop : -1.24 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 188 TYR 0.014 0.001 TYR R 219 PHE 0.009 0.001 PHE R 256 TRP 0.007 0.001 TRP R 195 HIS 0.002 0.000 HIS R 302 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 3286) covalent geometry : angle 0.55785 ( 4473) SS BOND : bond 0.00157 ( 2) SS BOND : angle 0.48867 ( 4) hydrogen bonds : bond 0.06057 ( 195) hydrogen bonds : angle 4.72488 ( 564) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.123 Fit side-chains outliers start: 10 outliers final: 10 residues processed: 43 average time/residue: 0.0541 time to fit residues: 3.0616 Evaluate side-chains 48 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 200 GLN Chi-restraints excluded: chain R residue 202 GLN Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain N residue 36 MET Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 103 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 36 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 GLN R 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.186061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.142957 restraints weight = 3631.470| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.34 r_work: 0.3523 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3288 Z= 0.157 Angle : 0.573 9.099 4477 Z= 0.297 Chirality : 0.041 0.118 514 Planarity : 0.004 0.038 541 Dihedral : 13.714 129.109 542 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.05 % Allowed : 17.38 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.43), residues: 392 helix: 1.13 (0.34), residues: 229 sheet: 0.34 (0.86), residues: 37 loop : -1.22 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 188 TYR 0.014 0.001 TYR R 219 PHE 0.010 0.001 PHE R 256 TRP 0.007 0.001 TRP R 195 HIS 0.002 0.001 HIS R 302 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 3286) covalent geometry : angle 0.57253 ( 4473) SS BOND : bond 0.00119 ( 2) SS BOND : angle 0.54125 ( 4) hydrogen bonds : bond 0.06133 ( 195) hydrogen bonds : angle 4.74769 ( 564) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.123 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 41 average time/residue: 0.0506 time to fit residues: 2.7370 Evaluate side-chains 45 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 202 GLN Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain N residue 36 MET Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 103 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 0.0970 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.186652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.143478 restraints weight = 3659.046| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.38 r_work: 0.3529 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3288 Z= 0.147 Angle : 0.562 8.726 4477 Z= 0.292 Chirality : 0.041 0.117 514 Planarity : 0.004 0.038 541 Dihedral : 13.690 129.433 542 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.74 % Allowed : 17.99 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.43), residues: 392 helix: 1.18 (0.34), residues: 229 sheet: 0.34 (0.86), residues: 37 loop : -1.17 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 188 TYR 0.014 0.001 TYR R 219 PHE 0.010 0.001 PHE R 256 TRP 0.008 0.001 TRP R 195 HIS 0.002 0.001 HIS R 302 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 3286) covalent geometry : angle 0.56239 ( 4473) SS BOND : bond 0.00117 ( 2) SS BOND : angle 0.52131 ( 4) hydrogen bonds : bond 0.06009 ( 195) hydrogen bonds : angle 4.71477 ( 564) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1029.65 seconds wall clock time: 18 minutes 14.60 seconds (1094.60 seconds total)