Starting phenix.real_space_refine on Sat Apr 26 15:35:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggp_40016/04_2025/8ggp_40016.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggp_40016/04_2025/8ggp_40016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ggp_40016/04_2025/8ggp_40016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggp_40016/04_2025/8ggp_40016.map" model { file = "/net/cci-nas-00/data/ceres_data/8ggp_40016/04_2025/8ggp_40016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggp_40016/04_2025/8ggp_40016.cif" } resolution = 3.2 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= 0.027 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 13 5.16 5 C 1394 2.51 5 N 328 2.21 5 O 340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 2075 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2060 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 7, 'TRANS': 272} Chain breaks: 1 Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 6, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 115 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.20, per 1000 atoms: 1.06 Number of scatterers: 2075 At special positions: 0 Unit cell: (57.2682, 80.6961, 62.4744, 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 13 16.00 O 340 8.00 N 328 7.00 C 1394 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " 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: 0.50 Conformation dependent library (CDL) restraints added in 242.3 milliseconds 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 538 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 90.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.578A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 65 removed outlier: 3.781A pdb=" N GLN R 65 " --> pdb=" O GLU R 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 62 through 65' Processing helix chain 'R' and resid 66 through 85 removed outlier: 4.135A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 97 removed outlier: 4.202A pdb=" N PHE R 89 " --> pdb=" O ALA R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.501A pdb=" N SER R 120 " --> pdb=" O CYS R 116 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.778A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 178 through 187 removed outlier: 3.520A pdb=" N ILE R 182 " --> pdb=" O HIS R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.718A pdb=" N VAL R 206 " --> pdb=" O ALA R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 237 Processing helix chain 'R' and resid 271 through 299 removed outlier: 4.093A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.508A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.821A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 318 through 320 No H-bonds generated for 'chain 'R' and resid 318 through 320' Processing helix chain 'R' and resid 321 through 327 Processing helix chain 'R' and resid 329 through 340 166 hydrogen bonds defined for protein. 498 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: 0.56 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 615 1.34 - 1.46: 495 1.46 - 1.58: 1004 1.58 - 1.70: 0 1.70 - 1.82: 17 Bond restraints: 2131 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.448 -0.051 2.00e-02 2.50e+03 6.50e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.442 -0.048 2.00e-02 2.50e+03 5.73e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.569 -0.046 2.00e-02 2.50e+03 5.25e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.562 -0.042 2.00e-02 2.50e+03 4.47e+00 bond pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " ideal model delta sigma weight residual 1.506 1.537 -0.031 2.00e-02 2.50e+03 2.44e+00 ... (remaining 2126 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 2813 1.08 - 2.16: 100 2.16 - 3.25: 8 3.25 - 4.33: 7 4.33 - 5.41: 5 Bond angle restraints: 2933 Sorted by residual: angle pdb=" C SER R 207 " pdb=" N PHE R 208 " pdb=" CA PHE R 208 " ideal model delta sigma weight residual 122.46 119.21 3.25 1.80e+00 3.09e-01 3.26e+00 angle pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 112.63 118.04 -5.41 3.00e+00 1.11e-01 3.25e+00 angle pdb=" N VAL R 87 " pdb=" CA VAL R 87 " pdb=" C VAL R 87 " ideal model delta sigma weight residual 108.88 112.53 -3.65 2.16e+00 2.14e-01 2.86e+00 angle pdb=" C THR R 96 " pdb=" N LYS R 97 " pdb=" CA LYS R 97 " ideal model delta sigma weight residual 124.31 127.13 -2.82 1.67e+00 3.59e-01 2.85e+00 angle pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " pdb=" CAI G1I R 501 " ideal model delta sigma weight residual 110.89 115.86 -4.97 3.00e+00 1.11e-01 2.75e+00 ... (remaining 2928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.65: 1053 12.65 - 25.30: 111 25.30 - 37.95: 28 37.95 - 50.60: 12 50.60 - 63.25: 1 Dihedral angle restraints: 1205 sinusoidal: 378 harmonic: 827 Sorted by residual: dihedral pdb=" CA PHE R 208 " pdb=" C PHE R 208 " pdb=" N TYR R 209 " pdb=" CA TYR R 209 " ideal model delta harmonic sigma weight residual -180.00 -162.43 -17.57 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA VAL R 295 " pdb=" C VAL R 295 " pdb=" N HIS R 296 " pdb=" CA HIS R 296 " ideal model delta harmonic sigma weight residual 180.00 -164.96 -15.04 0 5.00e+00 4.00e-02 9.04e+00 dihedral pdb=" CA ARG R 151 " pdb=" CB ARG R 151 " pdb=" CG ARG R 151 " pdb=" CD ARG R 151 " ideal model delta sinusoidal sigma weight residual -180.00 -130.02 -49.98 3 1.50e+01 4.44e-03 8.84e+00 ... (remaining 1202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 226 0.030 - 0.059: 101 0.059 - 0.089: 25 0.089 - 0.119: 14 0.119 - 0.149: 1 Chirality restraints: 367 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA TRP R 313 " pdb=" N TRP R 313 " pdb=" C TRP R 313 " pdb=" CB TRP R 313 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.42e-01 chirality pdb=" CA PRO R 138 " pdb=" N PRO R 138 " pdb=" C PRO R 138 " pdb=" CB PRO R 138 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.05e-01 ... (remaining 364 not shown) Planarity restraints: 351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 313 " -0.007 2.00e-02 2.50e+03 9.51e-03 2.26e+00 pdb=" CG TRP R 313 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP R 313 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP R 313 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 313 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP R 313 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 313 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 313 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 313 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 313 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 322 " 0.016 5.00e-02 4.00e+02 2.37e-02 8.98e-01 pdb=" N PRO R 323 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO R 323 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO R 323 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 210 " 0.014 5.00e-02 4.00e+02 2.10e-02 7.03e-01 pdb=" N PRO R 211 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " 0.012 5.00e-02 4.00e+02 ... (remaining 348 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 590 2.82 - 3.34: 2039 3.34 - 3.86: 3309 3.86 - 4.38: 3397 4.38 - 4.90: 6312 Nonbonded interactions: 15647 Sorted by model distance: nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.298 3.040 nonbonded pdb=" O LEU R 64 " pdb=" ND2 ASN R 69 " model vdw 2.305 3.120 nonbonded pdb=" O SER R 137 " pdb=" OG SER R 137 " model vdw 2.344 3.040 nonbonded pdb=" O THR R 189 " pdb=" OG1 THR R 189 " model vdw 2.491 3.040 nonbonded pdb=" OD1 ASN R 196 " pdb=" N GLN R 197 " model vdw 2.513 3.120 ... (remaining 15642 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.510 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.040 Process input model: 10.170 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 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 : 0.004 0.051 2132 Z= 0.189 Angle : 0.522 5.412 2935 Z= 0.285 Chirality : 0.039 0.149 367 Planarity : 0.003 0.024 351 Dihedral : 12.492 63.247 664 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: 1.89 (0.51), residues: 276 helix: 1.93 (0.35), residues: 220 sheet: None (None), residues: 0 loop : -1.52 (0.69), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 313 HIS 0.003 0.001 HIS R 93 PHE 0.010 0.001 PHE R 217 TYR 0.010 0.001 TYR R 174 ARG 0.001 0.000 ARG R 63 Details of bonding type rmsd hydrogen bonds : bond 0.16196 ( 166) hydrogen bonds : angle 5.18511 ( 498) SS BOND : bond 0.00127 ( 1) SS BOND : angle 1.45246 ( 2) covalent geometry : bond 0.00386 ( 2131) covalent geometry : angle 0.52046 ( 2933) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.240 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1285 time to fit residues: 3.1485 Evaluate side-chains 17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.132673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.116627 restraints weight = 2932.488| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.71 r_work: 0.3261 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.0807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2132 Z= 0.146 Angle : 0.481 5.464 2935 Z= 0.271 Chirality : 0.038 0.130 367 Planarity : 0.003 0.022 351 Dihedral : 4.298 17.933 309 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.52 % Allowed : 5.67 % Favored : 93.81 % 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: 2.27 (0.51), residues: 276 helix: 2.15 (0.35), residues: 226 sheet: None (None), residues: 0 loop : -1.66 (0.75), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 313 HIS 0.003 0.001 HIS R 296 PHE 0.009 0.001 PHE R 217 TYR 0.007 0.001 TYR R 308 ARG 0.001 0.000 ARG R 63 Details of bonding type rmsd hydrogen bonds : bond 0.06276 ( 166) hydrogen bonds : angle 3.94270 ( 498) SS BOND : bond 0.00128 ( 1) SS BOND : angle 1.28593 ( 2) covalent geometry : bond 0.00312 ( 2131) covalent geometry : angle 0.48024 ( 2933) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.197 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.1109 time to fit residues: 2.6457 Evaluate side-chains 16 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 5 optimal weight: 0.9990 chunk 26 optimal weight: 0.0270 chunk 23 optimal weight: 0.0570 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 overall best weight: 0.5756 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.132167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.115972 restraints weight = 2875.125| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.75 r_work: 0.3295 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2132 Z= 0.138 Angle : 0.463 5.451 2935 Z= 0.259 Chirality : 0.038 0.127 367 Planarity : 0.003 0.023 351 Dihedral : 4.268 17.964 309 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.03 % Allowed : 10.31 % Favored : 88.66 % 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: 2.47 (0.51), residues: 276 helix: 2.31 (0.35), residues: 226 sheet: None (None), residues: 0 loop : -1.66 (0.76), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 313 HIS 0.003 0.001 HIS R 296 PHE 0.009 0.001 PHE R 217 TYR 0.007 0.001 TYR R 174 ARG 0.001 0.000 ARG R 63 Details of bonding type rmsd hydrogen bonds : bond 0.05968 ( 166) hydrogen bonds : angle 3.75252 ( 498) SS BOND : bond 0.00157 ( 1) SS BOND : angle 1.26496 ( 2) covalent geometry : bond 0.00298 ( 2131) covalent geometry : angle 0.46167 ( 2933) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.218 Fit side-chains REVERT: R 40 MET cc_start: 0.7187 (mtt) cc_final: 0.6928 (mtt) outliers start: 2 outliers final: 2 residues processed: 17 average time/residue: 0.1802 time to fit residues: 3.7258 Evaluate side-chains 17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 178 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.131613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.115613 restraints weight = 2848.499| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.71 r_work: 0.3307 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2132 Z= 0.144 Angle : 0.465 5.461 2935 Z= 0.261 Chirality : 0.038 0.126 367 Planarity : 0.003 0.026 351 Dihedral : 4.274 17.895 309 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.03 % Allowed : 13.40 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.51), residues: 276 helix: 2.32 (0.34), residues: 226 sheet: None (None), residues: 0 loop : -1.71 (0.77), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 313 HIS 0.003 0.001 HIS R 296 PHE 0.009 0.001 PHE R 217 TYR 0.006 0.001 TYR R 199 ARG 0.001 0.000 ARG R 63 Details of bonding type rmsd hydrogen bonds : bond 0.06131 ( 166) hydrogen bonds : angle 3.71877 ( 498) SS BOND : bond 0.00223 ( 1) SS BOND : angle 1.16214 ( 2) covalent geometry : bond 0.00317 ( 2131) covalent geometry : angle 0.46409 ( 2933) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.218 Fit side-chains REVERT: R 40 MET cc_start: 0.7265 (mtt) cc_final: 0.7020 (mtt) outliers start: 2 outliers final: 2 residues processed: 17 average time/residue: 0.1773 time to fit residues: 3.6677 Evaluate side-chains 17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.128462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.112415 restraints weight = 2981.681| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.75 r_work: 0.3260 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2132 Z= 0.170 Angle : 0.490 5.526 2935 Z= 0.276 Chirality : 0.039 0.127 367 Planarity : 0.003 0.027 351 Dihedral : 4.388 17.906 309 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.03 % Allowed : 14.95 % Favored : 84.02 % 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: 2.31 (0.51), residues: 276 helix: 2.22 (0.35), residues: 226 sheet: None (None), residues: 0 loop : -1.89 (0.76), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.004 0.001 HIS R 296 PHE 0.009 0.001 PHE R 282 TYR 0.007 0.001 TYR R 174 ARG 0.001 0.000 ARG R 63 Details of bonding type rmsd hydrogen bonds : bond 0.06798 ( 166) hydrogen bonds : angle 3.82178 ( 498) SS BOND : bond 0.00181 ( 1) SS BOND : angle 1.20426 ( 2) covalent geometry : bond 0.00392 ( 2131) covalent geometry : angle 0.48894 ( 2933) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.203 Fit side-chains REVERT: R 40 MET cc_start: 0.7389 (mtt) cc_final: 0.7129 (mtt) REVERT: R 63 ARG cc_start: 0.5331 (ttm-80) cc_final: 0.4285 (ttm-80) outliers start: 2 outliers final: 2 residues processed: 16 average time/residue: 0.1070 time to fit residues: 2.3268 Evaluate side-chains 16 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 0.0870 chunk 10 optimal weight: 0.3980 chunk 6 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.139844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.124063 restraints weight = 2779.599| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.77 r_work: 0.3272 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2132 Z= 0.124 Angle : 0.441 5.463 2935 Z= 0.246 Chirality : 0.037 0.123 367 Planarity : 0.003 0.027 351 Dihedral : 4.181 18.327 309 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.55 % Allowed : 14.95 % Favored : 83.51 % 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: 2.62 (0.52), residues: 276 helix: 2.46 (0.35), residues: 226 sheet: None (None), residues: 0 loop : -1.83 (0.77), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 313 HIS 0.002 0.001 HIS R 93 PHE 0.009 0.001 PHE R 217 TYR 0.006 0.001 TYR R 308 ARG 0.001 0.000 ARG R 63 Details of bonding type rmsd hydrogen bonds : bond 0.05539 ( 166) hydrogen bonds : angle 3.61049 ( 498) SS BOND : bond 0.00169 ( 1) SS BOND : angle 1.05784 ( 2) covalent geometry : bond 0.00254 ( 2131) covalent geometry : angle 0.44040 ( 2933) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.238 Fit side-chains REVERT: R 40 MET cc_start: 0.7192 (mtt) cc_final: 0.6931 (mtt) REVERT: R 63 ARG cc_start: 0.5015 (ttm-80) cc_final: 0.3956 (ttm-80) outliers start: 3 outliers final: 3 residues processed: 18 average time/residue: 0.1799 time to fit residues: 3.9600 Evaluate side-chains 18 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 20 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.132184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.116230 restraints weight = 2903.118| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.73 r_work: 0.3313 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2132 Z= 0.136 Angle : 0.453 5.485 2935 Z= 0.253 Chirality : 0.038 0.123 367 Planarity : 0.003 0.027 351 Dihedral : 4.204 17.942 309 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.06 % Allowed : 14.43 % Favored : 83.51 % 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: 2.60 (0.51), residues: 276 helix: 2.44 (0.35), residues: 226 sheet: None (None), residues: 0 loop : -1.86 (0.77), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.003 0.001 HIS R 296 PHE 0.008 0.001 PHE R 282 TYR 0.006 0.001 TYR R 199 ARG 0.001 0.000 ARG R 63 Details of bonding type rmsd hydrogen bonds : bond 0.05847 ( 166) hydrogen bonds : angle 3.64357 ( 498) SS BOND : bond 0.00184 ( 1) SS BOND : angle 1.03965 ( 2) covalent geometry : bond 0.00294 ( 2131) covalent geometry : angle 0.45185 ( 2933) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 15 time to evaluate : 0.204 Fit side-chains REVERT: R 40 MET cc_start: 0.7244 (mtt) cc_final: 0.7002 (mtt) REVERT: R 63 ARG cc_start: 0.5130 (ttm-80) cc_final: 0.3983 (ttm-80) outliers start: 4 outliers final: 3 residues processed: 19 average time/residue: 0.1691 time to fit residues: 3.8874 Evaluate side-chains 18 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 13 optimal weight: 0.0000 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 10 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.133743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.118070 restraints weight = 2954.908| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.71 r_work: 0.3297 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2132 Z= 0.116 Angle : 0.427 5.438 2935 Z= 0.238 Chirality : 0.037 0.120 367 Planarity : 0.003 0.027 351 Dihedral : 4.096 17.983 309 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.55 % Allowed : 14.95 % Favored : 83.51 % 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: 2.79 (0.51), residues: 276 helix: 2.58 (0.35), residues: 226 sheet: None (None), residues: 0 loop : -1.81 (0.76), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 313 HIS 0.003 0.001 HIS R 93 PHE 0.008 0.001 PHE R 217 TYR 0.006 0.001 TYR R 209 ARG 0.001 0.000 ARG R 63 Details of bonding type rmsd hydrogen bonds : bond 0.05183 ( 166) hydrogen bonds : angle 3.53942 ( 498) SS BOND : bond 0.00154 ( 1) SS BOND : angle 0.97249 ( 2) covalent geometry : bond 0.00230 ( 2131) covalent geometry : angle 0.42659 ( 2933) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.232 Fit side-chains REVERT: R 40 MET cc_start: 0.7015 (mtt) cc_final: 0.6780 (mtt) REVERT: R 63 ARG cc_start: 0.4948 (ttm-80) cc_final: 0.3798 (ttm-80) outliers start: 3 outliers final: 3 residues processed: 17 average time/residue: 0.1164 time to fit residues: 2.6831 Evaluate side-chains 17 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 0.0770 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 8 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.133204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.116943 restraints weight = 2971.181| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.83 r_work: 0.3268 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2132 Z= 0.125 Angle : 0.437 5.464 2935 Z= 0.244 Chirality : 0.037 0.121 367 Planarity : 0.003 0.027 351 Dihedral : 4.109 17.725 309 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.06 % Allowed : 14.95 % Favored : 82.99 % 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: 2.76 (0.51), residues: 276 helix: 2.60 (0.34), residues: 225 sheet: None (None), residues: 0 loop : -2.00 (0.76), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.002 0.001 HIS R 93 PHE 0.008 0.001 PHE R 282 TYR 0.006 0.001 TYR R 308 ARG 0.001 0.000 ARG R 63 Details of bonding type rmsd hydrogen bonds : bond 0.05455 ( 166) hydrogen bonds : angle 3.55906 ( 498) SS BOND : bond 0.00186 ( 1) SS BOND : angle 0.97476 ( 2) covalent geometry : bond 0.00261 ( 2131) covalent geometry : angle 0.43595 ( 2933) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.262 Fit side-chains REVERT: R 40 MET cc_start: 0.7093 (mtt) cc_final: 0.6844 (mtt) REVERT: R 63 ARG cc_start: 0.5201 (ttm-80) cc_final: 0.4020 (ttm-80) REVERT: R 115 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7858 (tp) outliers start: 4 outliers final: 3 residues processed: 18 average time/residue: 0.1058 time to fit residues: 2.5641 Evaluate side-chains 18 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 3 optimal weight: 0.0870 chunk 20 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.131776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.116056 restraints weight = 2885.237| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.71 r_work: 0.3266 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2132 Z= 0.135 Angle : 0.446 5.494 2935 Z= 0.250 Chirality : 0.038 0.124 367 Planarity : 0.003 0.027 351 Dihedral : 4.175 18.238 309 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.06 % Allowed : 15.46 % Favored : 82.47 % 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: 2.74 (0.51), residues: 276 helix: 2.59 (0.34), residues: 225 sheet: None (None), residues: 0 loop : -2.00 (0.77), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.003 0.001 HIS R 296 PHE 0.008 0.001 PHE R 282 TYR 0.006 0.001 TYR R 199 ARG 0.001 0.000 ARG R 63 Details of bonding type rmsd hydrogen bonds : bond 0.05808 ( 166) hydrogen bonds : angle 3.61116 ( 498) SS BOND : bond 0.00190 ( 1) SS BOND : angle 1.02074 ( 2) covalent geometry : bond 0.00290 ( 2131) covalent geometry : angle 0.44564 ( 2933) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 552 Ramachandran restraints generated. 276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 15 time to evaluate : 0.236 Fit side-chains REVERT: R 63 ARG cc_start: 0.5121 (ttm-80) cc_final: 0.3948 (ttm-80) REVERT: R 115 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7723 (tp) outliers start: 4 outliers final: 3 residues processed: 19 average time/residue: 0.1667 time to fit residues: 3.8369 Evaluate side-chains 19 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 15 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.0060 chunk 14 optimal weight: 0.0570 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.4114 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.134011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.118226 restraints weight = 2917.845| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.75 r_work: 0.3293 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2132 Z= 0.115 Angle : 0.427 5.444 2935 Z= 0.237 Chirality : 0.037 0.119 367 Planarity : 0.003 0.027 351 Dihedral : 4.072 18.286 309 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.06 % Allowed : 15.46 % Favored : 82.47 % 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: 2.87 (0.52), residues: 276 helix: 2.65 (0.34), residues: 226 sheet: None (None), residues: 0 loop : -1.88 (0.80), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 313 HIS 0.003 0.001 HIS R 93 PHE 0.008 0.001 PHE R 217 TYR 0.006 0.001 TYR R 209 ARG 0.001 0.000 ARG R 63 Details of bonding type rmsd hydrogen bonds : bond 0.05169 ( 166) hydrogen bonds : angle 3.52069 ( 498) SS BOND : bond 0.00175 ( 1) SS BOND : angle 0.96790 ( 2) covalent geometry : bond 0.00231 ( 2131) covalent geometry : angle 0.42617 ( 2933) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1616.73 seconds wall clock time: 28 minutes 39.32 seconds (1719.32 seconds total)