Starting phenix.real_space_refine on Wed Sep 17 04:51:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fh0_50435/09_2025/9fh0_50435.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fh0_50435/09_2025/9fh0_50435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fh0_50435/09_2025/9fh0_50435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fh0_50435/09_2025/9fh0_50435.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fh0_50435/09_2025/9fh0_50435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fh0_50435/09_2025/9fh0_50435.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 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 25 5.16 5 C 2893 2.51 5 N 760 2.21 5 O 825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4503 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2152 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 261} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2351 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 8, 'TRANS': 304} Chain breaks: 2 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 11, 'ASN:plan1': 6, 'GLN:plan1': 2, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 97 Time building chain proxies: 1.47, per 1000 atoms: 0.33 Number of scatterers: 4503 At special positions: 0 Unit cell: (79.148, 66.518, 95.146, 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 25 16.00 O 825 8.00 N 760 7.00 C 2893 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.38 Conformation dependent library (CDL) restraints added in 187.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1106 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 2 sheets defined 65.8% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 26 through 30 Processing helix chain 'A' and resid 34 through 49 Processing helix chain 'A' and resid 88 through 110 removed outlier: 4.695A pdb=" N ALA A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ARG A 100 " --> pdb=" O ASN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 149 through 154 Processing helix chain 'A' and resid 160 through 170 Proline residue: A 166 - end of helix Processing helix chain 'A' and resid 170 through 180 removed outlier: 3.828A pdb=" N PHE A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 192 Processing helix chain 'A' and resid 205 through 221 removed outlier: 3.665A pdb=" N PHE A 209 " --> pdb=" O ASN A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 238 removed outlier: 3.671A pdb=" N CYS A 229 " --> pdb=" O TYR A 225 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 255 removed outlier: 3.719A pdb=" N ASN A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 262 removed outlier: 3.676A pdb=" N GLY A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'G' and resid 291 through 296 removed outlier: 4.829A pdb=" N ASN G 296 " --> pdb=" O GLY G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 325 Processing helix chain 'G' and resid 328 through 343 removed outlier: 3.519A pdb=" N ALA G 332 " --> pdb=" O LYS G 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 346 through 360 Processing helix chain 'G' and resid 362 through 377 Processing helix chain 'G' and resid 380 through 395 removed outlier: 3.921A pdb=" N MET G 384 " --> pdb=" O ASN G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 412 Processing helix chain 'G' and resid 412 through 421 Processing helix chain 'G' and resid 436 through 451 Processing helix chain 'G' and resid 459 through 471 Processing helix chain 'G' and resid 472 through 486 removed outlier: 3.755A pdb=" N THR G 476 " --> pdb=" O ASP G 472 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL G 486 " --> pdb=" O SER G 482 " (cutoff:3.500A) Processing helix chain 'G' and resid 491 through 504 Processing helix chain 'G' and resid 506 through 521 Processing helix chain 'G' and resid 524 through 538 removed outlier: 3.585A pdb=" N ARG G 528 " --> pdb=" O PHE G 524 " (cutoff:3.500A) Processing helix chain 'G' and resid 541 through 556 Processing helix chain 'G' and resid 578 through 589 removed outlier: 3.593A pdb=" N MET G 588 " --> pdb=" O VAL G 584 " (cutoff:3.500A) Processing helix chain 'G' and resid 590 through 595 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 16 removed outlier: 4.050A pdb=" N LYS A 197 " --> pdb=" O VAL A 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 123 through 124 removed outlier: 6.764A pdb=" N ALA A 123 " --> pdb=" O LEU A 147 " (cutoff:3.500A) 270 hydrogen bonds defined for protein. 795 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: 0.81 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1057 1.33 - 1.45: 928 1.45 - 1.57: 2568 1.57 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 4592 Sorted by residual: bond pdb=" CB ILE A 21 " pdb=" CG2 ILE A 21 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.69e+00 bond pdb=" CB ASN A 120 " pdb=" CG ASN A 120 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.46e+00 bond pdb=" CB VAL A 163 " pdb=" CG2 VAL A 163 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.43e+00 bond pdb=" CG LYS A 233 " pdb=" CD LYS A 233 " ideal model delta sigma weight residual 1.520 1.469 0.051 3.00e-02 1.11e+03 2.94e+00 bond pdb=" CG LEU A 45 " pdb=" CD2 LEU A 45 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.87e+00 ... (remaining 4587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 5770 1.47 - 2.94: 385 2.94 - 4.41: 38 4.41 - 5.88: 15 5.88 - 7.35: 8 Bond angle restraints: 6216 Sorted by residual: angle pdb=" C GLU A 251 " pdb=" N VAL A 252 " pdb=" CA VAL A 252 " ideal model delta sigma weight residual 120.64 116.07 4.57 1.66e+00 3.63e-01 7.57e+00 angle pdb=" C ARG A 269 " pdb=" N GLN A 270 " pdb=" CA GLN A 270 " ideal model delta sigma weight residual 121.94 116.69 5.25 2.00e+00 2.50e-01 6.89e+00 angle pdb=" C SER A 164 " pdb=" N LEU A 165 " pdb=" CA LEU A 165 " ideal model delta sigma weight residual 121.80 115.56 6.24 2.44e+00 1.68e-01 6.54e+00 angle pdb=" C ASP G 490 " pdb=" N GLU G 491 " pdb=" CA GLU G 491 " ideal model delta sigma weight residual 122.79 118.24 4.55 1.78e+00 3.16e-01 6.53e+00 angle pdb=" C ASN G 360 " pdb=" N GLU G 361 " pdb=" CA GLU G 361 " ideal model delta sigma weight residual 122.74 126.25 -3.51 1.44e+00 4.82e-01 5.94e+00 ... (remaining 6211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 2490 17.38 - 34.76: 207 34.76 - 52.14: 40 52.14 - 69.52: 9 69.52 - 86.90: 2 Dihedral angle restraints: 2748 sinusoidal: 1037 harmonic: 1711 Sorted by residual: dihedral pdb=" CA THR G 576 " pdb=" C THR G 576 " pdb=" N VAL G 577 " pdb=" CA VAL G 577 " ideal model delta harmonic sigma weight residual -180.00 -156.76 -23.24 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA TYR G 287 " pdb=" C TYR G 287 " pdb=" N LEU G 288 " pdb=" CA LEU G 288 " ideal model delta harmonic sigma weight residual 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA ASP G 279 " pdb=" C ASP G 279 " pdb=" N ASP G 280 " pdb=" CA ASP G 280 " ideal model delta harmonic sigma weight residual 180.00 157.98 22.02 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 2745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 366 0.041 - 0.082: 238 0.082 - 0.123: 81 0.123 - 0.163: 14 0.163 - 0.204: 2 Chirality restraints: 701 Sorted by residual: chirality pdb=" CB ILE G 538 " pdb=" CA ILE G 538 " pdb=" CG1 ILE G 538 " pdb=" CG2 ILE G 538 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA SER A 238 " pdb=" N SER A 238 " pdb=" C SER A 238 " pdb=" CB SER A 238 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" CB ILE A 241 " pdb=" CA ILE A 241 " pdb=" CG1 ILE A 241 " pdb=" CG2 ILE A 241 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.57e-01 ... (remaining 698 not shown) Planarity restraints: 797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 94 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" C VAL A 94 " 0.037 2.00e-02 2.50e+03 pdb=" O VAL A 94 " -0.014 2.00e-02 2.50e+03 pdb=" N SER A 95 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 182 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO A 183 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 183 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 183 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 121 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO A 122 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 122 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 122 " -0.022 5.00e-02 4.00e+02 ... (remaining 794 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 94 2.68 - 3.23: 4387 3.23 - 3.79: 6924 3.79 - 4.34: 9598 4.34 - 4.90: 15917 Nonbonded interactions: 36920 Sorted by model distance: nonbonded pdb=" OH TYR G 316 " pdb=" OD2 ASP G 348 " model vdw 2.121 3.040 nonbonded pdb=" OD1 ASP A 49 " pdb=" OG SER A 112 " model vdw 2.133 3.040 nonbonded pdb=" O GLY G 608 " pdb=" OG SER G 611 " model vdw 2.139 3.040 nonbonded pdb=" OG1 THR A 162 " pdb=" OE2 GLU A 251 " model vdw 2.202 3.040 nonbonded pdb=" NH1 ARG A 14 " pdb=" OE2 GLU A 16 " model vdw 2.216 3.120 ... (remaining 36915 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: 6.490 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: 0.030 Process input model: 6.760 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: 0.010 Load rotamer database and sin/cos tables:8.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 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 : 0.013 0.083 4592 Z= 0.540 Angle : 0.828 7.345 6216 Z= 0.440 Chirality : 0.055 0.204 701 Planarity : 0.005 0.042 797 Dihedral : 13.667 86.901 1642 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.02 (0.29), residues: 575 helix: -1.33 (0.24), residues: 369 sheet: -1.21 (0.83), residues: 30 loop : -3.39 (0.35), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 526 TYR 0.012 0.002 TYR G 468 PHE 0.020 0.003 PHE G 524 TRP 0.010 0.002 TRP G 407 HIS 0.006 0.002 HIS G 346 Details of bonding type rmsd covalent geometry : bond 0.01316 ( 4592) covalent geometry : angle 0.82817 ( 6216) hydrogen bonds : bond 0.15431 ( 270) hydrogen bonds : angle 5.84489 ( 795) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.196 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.8008 time to fit residues: 45.2509 Evaluate side-chains 36 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 101 ASN A 141 ASN A 181 ASN A 278 HIS G 278 ASN G 312 ASN ** G 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 GLN G 444 GLN G 447 GLN ** G 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 503 ASN G 537 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.122648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.083412 restraints weight = 6812.139| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.71 r_work: 0.2791 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4592 Z= 0.131 Angle : 0.530 5.454 6216 Z= 0.281 Chirality : 0.041 0.179 701 Planarity : 0.004 0.038 797 Dihedral : 4.848 21.973 626 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.97 % Allowed : 10.72 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.33), residues: 575 helix: 0.37 (0.27), residues: 362 sheet: -0.46 (0.85), residues: 33 loop : -2.52 (0.39), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 352 TYR 0.010 0.001 TYR G 468 PHE 0.014 0.001 PHE G 310 TRP 0.008 0.001 TRP A 93 HIS 0.005 0.001 HIS G 346 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 4592) covalent geometry : angle 0.53026 ( 6216) hydrogen bonds : bond 0.04215 ( 270) hydrogen bonds : angle 4.28495 ( 795) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.184 Fit side-chains REVERT: A 215 GLU cc_start: 0.8130 (tp30) cc_final: 0.7825 (tp30) outliers start: 9 outliers final: 0 residues processed: 52 average time/residue: 0.7567 time to fit residues: 40.5731 Evaluate side-chains 40 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 45 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 HIS G 359 GLN G 422 GLN ** G 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.124352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.081676 restraints weight = 6646.845| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.59 r_work: 0.2829 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4592 Z= 0.143 Angle : 0.521 9.022 6216 Z= 0.272 Chirality : 0.041 0.188 701 Planarity : 0.004 0.034 797 Dihedral : 4.498 20.340 626 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.75 % Allowed : 13.57 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.35), residues: 575 helix: 1.10 (0.28), residues: 364 sheet: -0.23 (0.84), residues: 33 loop : -2.06 (0.42), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 418 TYR 0.009 0.001 TYR G 468 PHE 0.013 0.001 PHE G 310 TRP 0.008 0.001 TRP A 93 HIS 0.003 0.001 HIS G 346 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 4592) covalent geometry : angle 0.52104 ( 6216) hydrogen bonds : bond 0.04018 ( 270) hydrogen bonds : angle 4.00066 ( 795) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.197 Fit side-chains REVERT: A 101 ASN cc_start: 0.9107 (OUTLIER) cc_final: 0.8895 (m110) REVERT: A 215 GLU cc_start: 0.8168 (tp30) cc_final: 0.7876 (tp30) REVERT: A 230 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8923 (mp) outliers start: 8 outliers final: 0 residues processed: 48 average time/residue: 0.7270 time to fit residues: 36.0985 Evaluate side-chains 40 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 230 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 55 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.125730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.083076 restraints weight = 6642.887| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.60 r_work: 0.2838 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4592 Z= 0.125 Angle : 0.486 9.157 6216 Z= 0.253 Chirality : 0.040 0.214 701 Planarity : 0.003 0.035 797 Dihedral : 4.294 19.909 626 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.09 % Allowed : 14.66 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.36), residues: 575 helix: 1.54 (0.28), residues: 365 sheet: -0.08 (0.84), residues: 33 loop : -1.70 (0.45), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 352 TYR 0.008 0.001 TYR G 468 PHE 0.010 0.001 PHE G 524 TRP 0.007 0.001 TRP A 93 HIS 0.001 0.000 HIS A 23 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 4592) covalent geometry : angle 0.48609 ( 6216) hydrogen bonds : bond 0.03572 ( 270) hydrogen bonds : angle 3.83761 ( 795) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.194 Fit side-chains REVERT: A 215 GLU cc_start: 0.8162 (tp30) cc_final: 0.7845 (tp30) outliers start: 5 outliers final: 0 residues processed: 46 average time/residue: 0.7373 time to fit residues: 35.0356 Evaluate side-chains 40 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 270 GLN A 275 GLN ** G 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.125008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.082890 restraints weight = 6727.156| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.62 r_work: 0.2811 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4592 Z= 0.120 Angle : 0.471 8.247 6216 Z= 0.246 Chirality : 0.040 0.180 701 Planarity : 0.003 0.035 797 Dihedral : 4.184 19.141 626 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.19 % Allowed : 14.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.36), residues: 575 helix: 1.77 (0.28), residues: 364 sheet: -0.00 (0.84), residues: 33 loop : -1.70 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 269 TYR 0.008 0.001 TYR G 468 PHE 0.011 0.001 PHE A 97 TRP 0.007 0.001 TRP A 93 HIS 0.001 0.000 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 4592) covalent geometry : angle 0.47059 ( 6216) hydrogen bonds : bond 0.03511 ( 270) hydrogen bonds : angle 3.74976 ( 795) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.176 Fit side-chains REVERT: A 215 GLU cc_start: 0.8094 (tp30) cc_final: 0.7731 (tp30) outliers start: 10 outliers final: 1 residues processed: 51 average time/residue: 0.7003 time to fit residues: 36.8828 Evaluate side-chains 43 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 405 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 12 optimal weight: 0.1980 chunk 34 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 181 ASN A 270 GLN ** G 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.123775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.081509 restraints weight = 6767.028| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 1.63 r_work: 0.2814 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4592 Z= 0.184 Angle : 0.511 6.957 6216 Z= 0.266 Chirality : 0.042 0.161 701 Planarity : 0.004 0.033 797 Dihedral : 4.280 20.628 626 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.75 % Allowed : 15.10 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.36), residues: 575 helix: 1.75 (0.28), residues: 363 sheet: -0.09 (0.84), residues: 33 loop : -1.65 (0.45), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 269 TYR 0.010 0.001 TYR G 468 PHE 0.012 0.001 PHE A 97 TRP 0.008 0.001 TRP A 93 HIS 0.001 0.001 HIS A 23 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 4592) covalent geometry : angle 0.51054 ( 6216) hydrogen bonds : bond 0.04150 ( 270) hydrogen bonds : angle 3.84872 ( 795) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.196 Fit side-chains REVERT: A 215 GLU cc_start: 0.8137 (tp30) cc_final: 0.7771 (tp30) outliers start: 8 outliers final: 1 residues processed: 43 average time/residue: 0.7297 time to fit residues: 32.4506 Evaluate side-chains 40 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 56 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 0.0050 chunk 5 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN ** G 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.125678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.083910 restraints weight = 6681.867| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.58 r_work: 0.2863 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4592 Z= 0.111 Angle : 0.451 6.927 6216 Z= 0.237 Chirality : 0.039 0.162 701 Planarity : 0.003 0.035 797 Dihedral : 4.098 19.199 626 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.66 % Allowed : 16.19 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.37), residues: 575 helix: 1.95 (0.28), residues: 364 sheet: 0.05 (0.84), residues: 33 loop : -1.64 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 269 TYR 0.008 0.001 TYR G 468 PHE 0.010 0.001 PHE A 97 TRP 0.006 0.001 TRP A 93 HIS 0.001 0.000 HIS G 440 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 4592) covalent geometry : angle 0.45130 ( 6216) hydrogen bonds : bond 0.03270 ( 270) hydrogen bonds : angle 3.68148 ( 795) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.219 Fit side-chains REVERT: A 215 GLU cc_start: 0.8086 (tp30) cc_final: 0.7745 (tp30) outliers start: 3 outliers final: 1 residues processed: 46 average time/residue: 0.7164 time to fit residues: 34.0912 Evaluate side-chains 43 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 0.0020 overall best weight: 1.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN ** G 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.122925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.080654 restraints weight = 6719.946| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.60 r_work: 0.2800 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4592 Z= 0.202 Angle : 0.525 6.073 6216 Z= 0.274 Chirality : 0.042 0.147 701 Planarity : 0.004 0.033 797 Dihedral : 4.333 21.160 626 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.09 % Allowed : 16.63 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.36), residues: 575 helix: 1.83 (0.28), residues: 364 sheet: -0.17 (0.83), residues: 33 loop : -1.57 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 269 TYR 0.011 0.001 TYR G 468 PHE 0.012 0.001 PHE A 97 TRP 0.009 0.001 TRP A 93 HIS 0.002 0.001 HIS A 23 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 4592) covalent geometry : angle 0.52498 ( 6216) hydrogen bonds : bond 0.04406 ( 270) hydrogen bonds : angle 3.89505 ( 795) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.198 Fit side-chains REVERT: A 215 GLU cc_start: 0.8149 (tp30) cc_final: 0.7790 (tp30) outliers start: 5 outliers final: 1 residues processed: 42 average time/residue: 0.8029 time to fit residues: 34.8195 Evaluate side-chains 38 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 23 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN G 304 GLN ** G 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.125292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.083252 restraints weight = 6677.534| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.62 r_work: 0.2843 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 4592 Z= 0.117 Angle : 0.480 6.928 6216 Z= 0.255 Chirality : 0.039 0.154 701 Planarity : 0.003 0.035 797 Dihedral : 4.114 19.699 626 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.88 % Allowed : 17.29 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.36), residues: 575 helix: 1.97 (0.28), residues: 365 sheet: 0.02 (0.85), residues: 33 loop : -1.54 (0.45), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 269 TYR 0.010 0.001 TYR G 468 PHE 0.010 0.001 PHE A 97 TRP 0.005 0.001 TRP A 93 HIS 0.001 0.000 HIS A 23 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 4592) covalent geometry : angle 0.47983 ( 6216) hydrogen bonds : bond 0.03283 ( 270) hydrogen bonds : angle 3.71822 ( 795) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.188 Fit side-chains REVERT: A 215 GLU cc_start: 0.8067 (tp30) cc_final: 0.7698 (tp30) REVERT: G 471 ASP cc_start: 0.8551 (t0) cc_final: 0.7868 (t0) outliers start: 4 outliers final: 3 residues processed: 43 average time/residue: 0.7612 time to fit residues: 33.7606 Evaluate side-chains 44 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain G residue 374 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN G 304 GLN ** G 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.124813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.082839 restraints weight = 6682.458| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.62 r_work: 0.2843 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4592 Z= 0.124 Angle : 0.474 6.068 6216 Z= 0.250 Chirality : 0.040 0.146 701 Planarity : 0.003 0.034 797 Dihedral : 4.102 19.645 626 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.66 % Allowed : 17.07 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.36), residues: 575 helix: 2.02 (0.28), residues: 364 sheet: 0.05 (0.86), residues: 33 loop : -1.48 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 269 TYR 0.010 0.001 TYR G 468 PHE 0.011 0.001 PHE A 97 TRP 0.007 0.001 TRP A 93 HIS 0.001 0.000 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 4592) covalent geometry : angle 0.47414 ( 6216) hydrogen bonds : bond 0.03507 ( 270) hydrogen bonds : angle 3.72713 ( 795) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1150 Ramachandran restraints generated. 575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.191 Fit side-chains REVERT: A 215 GLU cc_start: 0.8075 (tp30) cc_final: 0.7708 (tp30) REVERT: G 310 PHE cc_start: 0.7469 (m-80) cc_final: 0.6888 (m-80) REVERT: G 471 ASP cc_start: 0.8548 (t0) cc_final: 0.7992 (t0) outliers start: 3 outliers final: 2 residues processed: 42 average time/residue: 0.7949 time to fit residues: 34.4785 Evaluate side-chains 41 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain G residue 374 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 30 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN G 304 GLN ** G 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 519 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.125496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.083349 restraints weight = 6709.773| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.63 r_work: 0.2848 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4592 Z= 0.111 Angle : 0.457 6.236 6216 Z= 0.241 Chirality : 0.039 0.151 701 Planarity : 0.003 0.035 797 Dihedral : 4.026 19.237 626 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.44 % Allowed : 17.72 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.37), residues: 575 helix: 2.08 (0.28), residues: 365 sheet: 0.11 (0.86), residues: 33 loop : -1.51 (0.45), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 269 TYR 0.009 0.001 TYR G 468 PHE 0.011 0.001 PHE A 97 TRP 0.007 0.001 TRP A 93 HIS 0.001 0.000 HIS A 23 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 4592) covalent geometry : angle 0.45693 ( 6216) hydrogen bonds : bond 0.03238 ( 270) hydrogen bonds : angle 3.66874 ( 795) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1936.94 seconds wall clock time: 33 minutes 50.31 seconds (2030.31 seconds total)