Starting phenix.real_space_refine on Wed Mar 5 18:08:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zpn_60350/03_2025/8zpn_60350.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zpn_60350/03_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_60350/03_2025/8zpn_60350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zpn_60350/03_2025/8zpn_60350.map" model { file = "/net/cci-nas-00/data/ceres_data/8zpn_60350/03_2025/8zpn_60350.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zpn_60350/03_2025/8zpn_60350.cif" } resolution = 3.31 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= 0.001 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-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: 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: 3.34, per 1000 atoms: 1.04 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: 0.98 Conformation dependent library (CDL) restraints added in 324.6 milliseconds 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: 0.35 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: 0.90 Time building geometry restraints manager: 1.12 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: 1.620 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.270 Find NCS groups from input model: 0.030 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.020 ------------------------------------------------------------------------------- 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 3286 Z= 0.227 Angle : 0.602 6.365 4473 Z= 0.303 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 (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: 0.32 (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 TRP 0.005 0.001 TRP R 195 HIS 0.004 0.001 HIS R 203 PHE 0.009 0.001 PHE R 256 TYR 0.011 0.001 TYR R 219 ARG 0.002 0.000 ARG R 77 *********************** 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 : 0.355 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1907 time to fit residues: 10.8123 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 : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.5980 chunk 29 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 0.0370 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- 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 = 0.4179 r_free = 0.4179 target = 0.193895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.150222 restraints weight = 3547.782| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.35 r_work: 0.3596 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3286 Z= 0.177 Angle : 0.539 5.586 4473 Z= 0.286 Chirality : 0.041 0.120 514 Planarity : 0.005 0.048 541 Dihedral : 21.022 170.223 542 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % 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 (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: 0.57 (0.42), residues: 392 helix: 1.30 (0.34), residues: 228 sheet: 0.50 (0.81), residues: 37 loop : -1.33 (0.55), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 113 HIS 0.002 0.001 HIS R 302 PHE 0.009 0.001 PHE R 256 TYR 0.014 0.001 TYR R 219 ARG 0.002 0.000 ARG N 68 *********************** 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 51 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: R 200 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7202 (tt0) outliers start: 9 outliers final: 6 residues processed: 45 average time/residue: 0.1794 time to fit residues: 9.7919 Evaluate side-chains 47 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 36 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 12 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 20 optimal weight: 0.0770 chunk 15 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.188194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.144573 restraints weight = 3510.790| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.36 r_work: 0.3538 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3286 Z= 0.215 Angle : 0.553 5.622 4473 Z= 0.289 Chirality : 0.042 0.118 514 Planarity : 0.004 0.045 541 Dihedral : 18.642 172.942 542 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.44 % Allowed : 11.89 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.42), residues: 392 helix: 1.24 (0.33), residues: 228 sheet: 0.63 (0.85), residues: 37 loop : -1.35 (0.56), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 113 HIS 0.002 0.001 HIS R 302 PHE 0.010 0.001 PHE R 256 TYR 0.014 0.001 TYR R 219 ARG 0.001 0.000 ARG R 70 *********************** 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 48 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.362 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 44 average time/residue: 0.1460 time to fit residues: 8.1651 Evaluate side-chains 45 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 32 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.190274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.145842 restraints weight = 3568.396| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.38 r_work: 0.3539 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3286 Z= 0.211 Angle : 0.534 5.587 4473 Z= 0.281 Chirality : 0.041 0.117 514 Planarity : 0.004 0.042 541 Dihedral : 17.299 173.464 542 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.05 % Allowed : 13.41 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.43), residues: 392 helix: 1.27 (0.34), residues: 228 sheet: 0.56 (0.86), residues: 37 loop : -1.35 (0.57), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 113 HIS 0.002 0.001 HIS R 203 PHE 0.010 0.001 PHE R 256 TYR 0.014 0.001 TYR R 219 ARG 0.001 0.000 ARG N 68 *********************** 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 49 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: R 200 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7489 (tt0) outliers start: 10 outliers final: 8 residues processed: 43 average time/residue: 0.1495 time to fit residues: 8.1550 Evaluate side-chains 46 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 231 LEU Chi-restraints excluded: chain R residue 254 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 13 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.185531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.142226 restraints weight = 3563.381| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.28 r_work: 0.3511 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3286 Z= 0.255 Angle : 0.563 5.650 4473 Z= 0.297 Chirality : 0.042 0.120 514 Planarity : 0.004 0.040 541 Dihedral : 16.432 152.480 542 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.35 % Allowed : 13.72 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.42), residues: 392 helix: 1.11 (0.33), residues: 227 sheet: 0.55 (0.86), residues: 37 loop : -1.43 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 195 HIS 0.002 0.001 HIS R 203 PHE 0.011 0.001 PHE R 256 TYR 0.016 0.001 TYR R 219 ARG 0.001 0.000 ARG R 70 *********************** 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 50 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.353 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 44 average time/residue: 0.1514 time to fit residues: 8.5071 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 : 0.345 ------------------------------------------------------------------------------- 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 231 LEU Chi-restraints excluded: chain R residue 254 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.186480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.143030 restraints weight = 3637.010| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.37 r_work: 0.3518 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3286 Z= 0.229 Angle : 0.546 5.600 4473 Z= 0.288 Chirality : 0.042 0.118 514 Planarity : 0.004 0.039 541 Dihedral : 15.205 128.815 542 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.13 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 (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: 0.38 (0.42), residues: 392 helix: 1.16 (0.33), residues: 227 sheet: 0.47 (0.86), residues: 37 loop : -1.44 (0.55), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 195 HIS 0.002 0.001 HIS R 203 PHE 0.010 0.001 PHE R 256 TYR 0.014 0.001 TYR R 219 ARG 0.001 0.000 ARG R 77 *********************** 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 50 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.352 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 44 average time/residue: 0.1529 time to fit residues: 8.5191 Evaluate side-chains 49 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 231 LEU Chi-restraints excluded: chain R residue 254 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.181821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.138698 restraints weight = 3571.118| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.27 r_work: 0.3475 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3286 Z= 0.316 Angle : 0.610 6.458 4473 Z= 0.321 Chirality : 0.044 0.126 514 Planarity : 0.004 0.038 541 Dihedral : 14.224 126.288 542 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.35 % Allowed : 14.63 % 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 (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: 0.06 (0.42), residues: 392 helix: 0.84 (0.33), residues: 227 sheet: 0.56 (0.87), residues: 37 loop : -1.53 (0.55), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 291 HIS 0.002 0.001 HIS R 203 PHE 0.013 0.002 PHE R 256 TYR 0.019 0.001 TYR R 219 ARG 0.002 0.000 ARG R 243 *********************** 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 49 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.324 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 42 average time/residue: 0.1507 time to fit residues: 8.0476 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 : 0.318 ------------------------------------------------------------------------------- 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 231 LEU Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 79 THR 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 30 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.185098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.141791 restraints weight = 3592.093| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.35 r_work: 0.3512 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3286 Z= 0.230 Angle : 0.561 8.045 4473 Z= 0.295 Chirality : 0.042 0.117 514 Planarity : 0.005 0.073 541 Dihedral : 13.904 128.099 542 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.35 % Allowed : 14.33 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.42), residues: 392 helix: 1.07 (0.34), residues: 227 sheet: 0.47 (0.87), residues: 37 loop : -1.47 (0.55), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 195 HIS 0.002 0.001 HIS R 302 PHE 0.010 0.001 PHE R 257 TYR 0.015 0.001 TYR R 219 ARG 0.012 0.000 ARG R 188 *********************** 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 47 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.326 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 40 average time/residue: 0.1280 time to fit residues: 6.7325 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 : 0.303 ------------------------------------------------------------------------------- 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 231 LEU Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain N residue 55 SER 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 34 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 0.0030 chunk 15 optimal weight: 0.0060 chunk 28 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.5008 ------------------------------------------------------------------------------- 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 = 0.4109 r_free = 0.4109 target = 0.187739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.144483 restraints weight = 3577.421| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.36 r_work: 0.3541 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3286 Z= 0.190 Angle : 0.539 9.436 4473 Z= 0.280 Chirality : 0.040 0.116 514 Planarity : 0.005 0.069 541 Dihedral : 13.758 131.310 542 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.44 % Allowed : 16.46 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.43), residues: 392 helix: 1.24 (0.34), residues: 228 sheet: 0.29 (0.84), residues: 37 loop : -1.35 (0.56), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 195 HIS 0.002 0.001 HIS R 203 PHE 0.009 0.001 PHE R 256 TYR 0.012 0.001 TYR R 219 ARG 0.010 0.000 ARG R 188 *********************** 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 41 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.331 Fit side-chains REVERT: R 202 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.7015 (pp30) outliers start: 8 outliers final: 6 residues processed: 36 average time/residue: 0.1463 time to fit residues: 7.0881 Evaluate side-chains 40 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 55 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.4063 r_free = 0.4063 target = 0.183022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.140209 restraints weight = 3539.311| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.26 r_work: 0.3494 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3286 Z= 0.288 Angle : 0.601 10.484 4473 Z= 0.312 Chirality : 0.043 0.124 514 Planarity : 0.005 0.062 541 Dihedral : 13.903 130.408 542 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.13 % Allowed : 16.77 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.42), residues: 392 helix: 1.00 (0.33), residues: 227 sheet: 0.40 (0.85), residues: 37 loop : -1.42 (0.55), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 195 HIS 0.002 0.001 HIS R 203 PHE 0.012 0.001 PHE R 256 TYR 0.018 0.001 TYR R 219 ARG 0.010 0.001 ARG R 188 ********************** 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 46 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.348 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 42 average time/residue: 0.1255 time to fit residues: 6.9157 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 : 0.341 ------------------------------------------------------------------------------- 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 55 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 2 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.185832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.142045 restraints weight = 3601.201| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.38 r_work: 0.3495 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3286 Z= 0.251 Angle : 0.584 10.175 4473 Z= 0.304 Chirality : 0.042 0.121 514 Planarity : 0.004 0.038 541 Dihedral : 13.871 129.743 542 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.74 % Allowed : 15.55 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.42), residues: 392 helix: 0.98 (0.33), residues: 227 sheet: 0.41 (0.84), residues: 37 loop : -1.43 (0.56), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 195 HIS 0.002 0.001 HIS R 203 PHE 0.011 0.001 PHE R 257 TYR 0.015 0.001 TYR R 219 ARG 0.004 0.000 ARG R 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2096.58 seconds wall clock time: 36 minutes 53.14 seconds (2213.14 seconds total)