Starting phenix.real_space_refine on Wed Jul 1 21:53:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ex4_28650/07_2026/8ex4_28650.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ex4_28650/07_2026/8ex4_28650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ex4_28650/07_2026/8ex4_28650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ex4_28650/07_2026/8ex4_28650.map" model { file = "/net/cci-nas-00/data/ceres_data/8ex4_28650/07_2026/8ex4_28650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ex4_28650/07_2026/8ex4_28650.cif" } resolution = 2.93 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= 0.001 sd= 0.033 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 17 5.16 5 C 2122 2.51 5 N 532 2.21 5 O 554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3226 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3201 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 12, 'TRANS': 404} Chain breaks: 2 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'S1P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.75, per 1000 atoms: 0.23 Number of scatterers: 3226 At special positions: 0 Unit cell: (70.741, 68.794, 80.476, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 P 1 15.00 O 554 8.00 N 532 7.00 C 2122 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: 0.19 Conformation dependent library (CDL) restraints added in 83.4 milliseconds 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 0 sheets defined 93.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'A' and resid 99 through 118 Processing helix chain 'A' and resid 119 through 124 removed outlier: 4.282A pdb=" N ALA A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 136 through 165 removed outlier: 4.221A pdb=" N GLN A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 153 " --> pdb=" O CYS A 149 " (cutoff:3.500A) Proline residue: A 156 - end of helix removed outlier: 4.061A pdb=" N ASP A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG A 164 " --> pdb=" O TYR A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 186 Processing helix chain 'A' and resid 192 through 222 removed outlier: 3.770A pdb=" N LEU A 196 " --> pdb=" O TYR A 192 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 223 through 257 removed outlier: 3.675A pdb=" N ALA A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix Processing helix chain 'A' and resid 259 through 266 removed outlier: 4.171A pdb=" N LEU A 263 " --> pdb=" O TRP A 259 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 280 removed outlier: 3.658A pdb=" N ILE A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 removed outlier: 4.031A pdb=" N ARG A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 347 Proline residue: A 337 - end of helix Processing helix chain 'A' and resid 361 through 389 Processing helix chain 'A' and resid 394 through 418 removed outlier: 3.781A pdb=" N ILE A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 437 Processing helix chain 'A' and resid 439 through 451 removed outlier: 3.601A pdb=" N THR A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA A 444 " --> pdb=" O TRP A 440 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 470 removed outlier: 4.526A pdb=" N ALA A 457 " --> pdb=" O PRO A 453 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N THR A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 489 removed outlier: 3.603A pdb=" N SER A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 506 Processing helix chain 'A' and resid 506 through 538 removed outlier: 4.109A pdb=" N PHE A 510 " --> pdb=" O MET A 506 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N SER A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) 273 hydrogen bonds defined for protein. 819 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: 0.54 Time building geometry restraints manager: 0.26 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: 922 1.34 - 1.45: 541 1.45 - 1.57: 1809 1.57 - 1.69: 1 1.69 - 1.81: 26 Bond restraints: 3299 Sorted by residual: bond pdb=" O1 S1P A 601 " pdb=" P22 S1P A 601 " ideal model delta sigma weight residual 1.677 1.607 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C ILE A 238 " pdb=" N PRO A 239 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.20e-02 6.94e+03 2.82e+00 bond pdb=" CA ALA A 103 " pdb=" C ALA A 103 " ideal model delta sigma weight residual 1.524 1.504 0.020 1.26e-02 6.30e+03 2.50e+00 bond pdb=" CA LYS A 102 " pdb=" C LYS A 102 " ideal model delta sigma weight residual 1.523 1.502 0.021 1.37e-02 5.33e+03 2.30e+00 bond pdb=" C PHE A 176 " pdb=" O PHE A 176 " ideal model delta sigma weight residual 1.236 1.220 0.017 1.15e-02 7.56e+03 2.07e+00 ... (remaining 3294 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 4279 1.51 - 3.03: 143 3.03 - 4.54: 31 4.54 - 6.06: 19 6.06 - 7.57: 2 Bond angle restraints: 4474 Sorted by residual: angle pdb=" C ILE A 175 " pdb=" CA ILE A 175 " pdb=" CB ILE A 175 " ideal model delta sigma weight residual 111.81 107.03 4.78 1.25e+00 6.40e-01 1.46e+01 angle pdb=" CA TRP A 178 " pdb=" CB TRP A 178 " pdb=" CG TRP A 178 " ideal model delta sigma weight residual 113.60 120.11 -6.51 1.90e+00 2.77e-01 1.17e+01 angle pdb=" N LYS A 102 " pdb=" CA LYS A 102 " pdb=" C LYS A 102 " ideal model delta sigma weight residual 112.23 108.32 3.91 1.26e+00 6.30e-01 9.63e+00 angle pdb=" N PHE A 222 " pdb=" CA PHE A 222 " pdb=" C PHE A 222 " ideal model delta sigma weight residual 109.81 114.21 -4.40 1.53e+00 4.27e-01 8.28e+00 angle pdb=" N THR A 226 " pdb=" CA THR A 226 " pdb=" C THR A 226 " ideal model delta sigma weight residual 111.28 108.19 3.09 1.09e+00 8.42e-01 8.01e+00 ... (remaining 4469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.69: 1847 29.69 - 59.37: 49 59.37 - 89.05: 8 89.05 - 118.74: 1 118.74 - 148.42: 7 Dihedral angle restraints: 1912 sinusoidal: 725 harmonic: 1187 Sorted by residual: dihedral pdb=" C2 S1P A 601 " pdb=" C1 S1P A 601 " pdb=" O1 S1P A 601 " pdb=" P22 S1P A 601 " ideal model delta sinusoidal sigma weight residual 262.13 113.71 148.42 1 3.00e+01 1.11e-03 1.98e+01 dihedral pdb=" N2 S1P A 601 " pdb=" C1 S1P A 601 " pdb=" C2 S1P A 601 " pdb=" O1 S1P A 601 " ideal model delta sinusoidal sigma weight residual -73.93 58.08 -132.01 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" C11 S1P A 601 " pdb=" C10 S1P A 601 " pdb=" C9 S1P A 601 " pdb=" C8 S1P A 601 " ideal model delta sinusoidal sigma weight residual 65.14 -166.80 -128.06 1 3.00e+01 1.11e-03 1.72e+01 ... (remaining 1909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 371 0.042 - 0.083: 123 0.083 - 0.124: 28 0.124 - 0.165: 1 0.165 - 0.207: 2 Chirality restraints: 525 Sorted by residual: chirality pdb=" CA TRP A 178 " pdb=" N TRP A 178 " pdb=" C TRP A 178 " pdb=" CB TRP A 178 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB VAL A 125 " pdb=" CA VAL A 125 " pdb=" CG1 VAL A 125 " pdb=" CG2 VAL A 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA SER A 266 " pdb=" N SER A 266 " pdb=" C SER A 266 " pdb=" CB SER A 266 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 522 not shown) Planarity restraints: 544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 178 " 0.014 2.00e-02 2.50e+03 1.02e-02 2.62e+00 pdb=" CG TRP A 178 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP A 178 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 178 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 178 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 178 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 178 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 178 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 178 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 178 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 266 " 0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO A 267 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 267 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 267 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 508 " -0.020 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO A 509 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 509 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 509 " -0.017 5.00e-02 4.00e+02 ... (remaining 541 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 87 2.71 - 3.26: 3492 3.26 - 3.81: 5487 3.81 - 4.35: 7165 4.35 - 4.90: 11955 Nonbonded interactions: 28186 Sorted by model distance: nonbonded pdb=" O LEU A 127 " pdb=" NE2 GLN A 131 " model vdw 2.165 3.120 nonbonded pdb=" OH TYR A 246 " pdb=" O GLY A 333 " model vdw 2.217 3.040 nonbonded pdb=" OD1 ASP A 529 " pdb=" NH2 ARG A 532 " model vdw 2.248 3.120 nonbonded pdb=" O ILE A 369 " pdb=" OG1 THR A 373 " model vdw 2.254 3.040 nonbonded pdb=" OD1 ASP A 484 " pdb=" NH2 ARG A 487 " model vdw 2.280 3.120 ... (remaining 28181 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: 4.690 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.990 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 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 : 0.005 0.070 3299 Z= 0.249 Angle : 0.753 7.570 4474 Z= 0.429 Chirality : 0.043 0.207 525 Planarity : 0.004 0.030 544 Dihedral : 17.094 148.420 1152 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % 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 are not related in a simple way. whole: 0.40 (0.41), residues: 411 helix: 0.41 (0.27), residues: 363 sheet: None (None), residues: 0 loop : 0.08 (0.99), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 389 TYR 0.013 0.001 TYR A 120 PHE 0.017 0.002 PHE A 236 TRP 0.028 0.002 TRP A 178 HIS 0.004 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.25 ( 3299) covalent geometry : angle 0.75266 / 0.43 ( 4474) hydrogen bonds : bond 0.14561 / 9.35 ( 273) hydrogen bonds : angle 6.29681 / 4.34 ( 819) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.109 Fit side-chains REVERT: A 488 GLN cc_start: 0.7754 (mt0) cc_final: 0.7540 (mt0) outliers start: 0 outliers final: 1 residues processed: 57 average time/residue: 0.3642 time to fit residues: 21.4643 Evaluate side-chains 45 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 GLN A 536 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.162607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.140019 restraints weight = 3353.311| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.23 r_work: 0.3507 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3299 Z= 0.168 Angle : 0.581 8.685 4474 Z= 0.308 Chirality : 0.040 0.163 525 Planarity : 0.004 0.032 544 Dihedral : 15.911 152.576 474 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.08 % Allowed : 5.93 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.41), residues: 411 helix: 0.98 (0.26), residues: 369 sheet: None (None), residues: 0 loop : -0.26 (0.98), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 389 TYR 0.013 0.001 TYR A 120 PHE 0.025 0.002 PHE A 236 TRP 0.038 0.002 TRP A 178 HIS 0.004 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 ( 3299) covalent geometry : angle 0.58126 / 0.31 ( 4474) hydrogen bonds : bond 0.05621 / 3.79 ( 273) hydrogen bonds : angle 4.54186 / 3.19 ( 819) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.071 Fit side-chains REVERT: A 488 GLN cc_start: 0.7470 (mt0) cc_final: 0.7189 (mt0) outliers start: 7 outliers final: 3 residues processed: 49 average time/residue: 0.2355 time to fit residues: 12.0793 Evaluate side-chains 43 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 485 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 0.0570 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 GLN A 536 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.171631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.150037 restraints weight = 3260.834| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.17 r_work: 0.3542 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3299 Z= 0.133 Angle : 0.517 7.667 4474 Z= 0.276 Chirality : 0.038 0.155 525 Planarity : 0.004 0.035 544 Dihedral : 15.844 163.273 472 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.48 % Allowed : 9.50 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.41), residues: 411 helix: 1.43 (0.27), residues: 370 sheet: None (None), residues: 0 loop : 0.11 (1.01), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 389 TYR 0.011 0.001 TYR A 120 PHE 0.024 0.001 PHE A 236 TRP 0.029 0.002 TRP A 178 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 3299) covalent geometry : angle 0.51746 / 0.28 ( 4474) hydrogen bonds : bond 0.04942 / 3.34 ( 273) hydrogen bonds : angle 4.29788 / 3.02 ( 819) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.101 Fit side-chains REVERT: A 218 ILE cc_start: 0.8270 (mt) cc_final: 0.7989 (mp) REVERT: A 488 GLN cc_start: 0.7450 (mt0) cc_final: 0.7154 (mt0) outliers start: 5 outliers final: 4 residues processed: 50 average time/residue: 0.2746 time to fit residues: 14.5022 Evaluate side-chains 47 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 524 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.168651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.147019 restraints weight = 3268.355| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.16 r_work: 0.3510 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3299 Z= 0.163 Angle : 0.553 8.289 4474 Z= 0.296 Chirality : 0.039 0.164 525 Planarity : 0.004 0.034 544 Dihedral : 15.947 168.537 472 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.08 % Allowed : 10.98 % Favored : 86.94 % 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 are not related in a simple way. whole: 1.82 (0.41), residues: 411 helix: 1.39 (0.26), residues: 370 sheet: None (None), residues: 0 loop : 0.08 (1.01), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 389 TYR 0.012 0.001 TYR A 120 PHE 0.031 0.002 PHE A 236 TRP 0.034 0.002 TRP A 178 HIS 0.005 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 3299) covalent geometry : angle 0.55322 / 0.30 ( 4474) hydrogen bonds : bond 0.05410 / 3.64 ( 273) hydrogen bonds : angle 4.36448 / 3.06 ( 819) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.068 Fit side-chains REVERT: A 218 ILE cc_start: 0.8228 (mt) cc_final: 0.7943 (mp) REVERT: A 488 GLN cc_start: 0.7345 (mt0) cc_final: 0.7050 (mt0) outliers start: 7 outliers final: 4 residues processed: 47 average time/residue: 0.2640 time to fit residues: 13.0258 Evaluate side-chains 48 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 485 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.167686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.146154 restraints weight = 3249.937| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.16 r_work: 0.3503 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3299 Z= 0.178 Angle : 0.572 8.358 4474 Z= 0.308 Chirality : 0.040 0.167 525 Planarity : 0.004 0.034 544 Dihedral : 15.784 158.400 472 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.08 % Allowed : 13.06 % Favored : 84.87 % 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 are not related in a simple way. whole: 1.75 (0.41), residues: 411 helix: 1.33 (0.26), residues: 370 sheet: None (None), residues: 0 loop : 0.14 (1.01), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 389 TYR 0.013 0.002 TYR A 120 PHE 0.012 0.002 PHE A 327 TRP 0.035 0.002 TRP A 178 HIS 0.006 0.002 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 ( 3299) covalent geometry : angle 0.57172 / 0.31 ( 4474) hydrogen bonds : bond 0.05582 / 3.76 ( 273) hydrogen bonds : angle 4.38616 / 3.07 ( 819) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.113 Fit side-chains REVERT: A 218 ILE cc_start: 0.8237 (mt) cc_final: 0.7940 (mp) REVERT: A 488 GLN cc_start: 0.7305 (mt0) cc_final: 0.6974 (mt0) outliers start: 7 outliers final: 5 residues processed: 49 average time/residue: 0.2881 time to fit residues: 14.9248 Evaluate side-chains 48 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 524 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 0.0870 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 18 optimal weight: 0.2980 chunk 2 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.165401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.143128 restraints weight = 3329.718| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.21 r_work: 0.3528 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3299 Z= 0.136 Angle : 0.529 7.829 4474 Z= 0.283 Chirality : 0.038 0.158 525 Planarity : 0.004 0.033 544 Dihedral : 15.063 157.660 472 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.78 % Allowed : 14.84 % Favored : 83.38 % 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 are not related in a simple way. whole: 2.07 (0.41), residues: 411 helix: 1.54 (0.26), residues: 371 sheet: None (None), residues: 0 loop : 0.21 (1.01), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 389 TYR 0.010 0.001 TYR A 120 PHE 0.010 0.001 PHE A 327 TRP 0.030 0.002 TRP A 178 HIS 0.005 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 ( 3299) covalent geometry : angle 0.52870 / 0.28 ( 4474) hydrogen bonds : bond 0.04988 / 3.37 ( 273) hydrogen bonds : angle 4.26623 / 2.99 ( 819) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.139 Fit side-chains REVERT: A 218 ILE cc_start: 0.8250 (mt) cc_final: 0.7958 (mp) outliers start: 6 outliers final: 3 residues processed: 45 average time/residue: 0.2692 time to fit residues: 12.8336 Evaluate side-chains 44 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 485 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 GLN A 488 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.162553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.139392 restraints weight = 3356.335| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.28 r_work: 0.3463 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3299 Z= 0.165 Angle : 0.563 8.235 4474 Z= 0.302 Chirality : 0.040 0.165 525 Planarity : 0.004 0.034 544 Dihedral : 14.612 158.523 472 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.67 % Allowed : 15.43 % Favored : 81.90 % 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 are not related in a simple way. whole: 1.90 (0.40), residues: 411 helix: 1.45 (0.26), residues: 369 sheet: None (None), residues: 0 loop : -0.01 (0.96), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 389 TYR 0.012 0.001 TYR A 120 PHE 0.012 0.001 PHE A 327 TRP 0.035 0.002 TRP A 178 HIS 0.006 0.002 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 3299) covalent geometry : angle 0.56338 / 0.30 ( 4474) hydrogen bonds : bond 0.05375 / 3.62 ( 273) hydrogen bonds : angle 4.35459 / 3.06 ( 819) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.070 Fit side-chains REVERT: A 218 ILE cc_start: 0.8145 (mt) cc_final: 0.7819 (mp) REVERT: A 248 THR cc_start: 0.8004 (m) cc_final: 0.7727 (m) outliers start: 9 outliers final: 4 residues processed: 45 average time/residue: 0.3088 time to fit residues: 14.6380 Evaluate side-chains 42 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 485 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 19 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.169146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.147616 restraints weight = 3311.290| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.17 r_work: 0.3514 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3299 Z= 0.163 Angle : 0.566 8.105 4474 Z= 0.303 Chirality : 0.040 0.164 525 Planarity : 0.004 0.035 544 Dihedral : 14.320 157.840 472 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.08 % Allowed : 16.02 % Favored : 81.90 % 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 are not related in a simple way. whole: 1.87 (0.40), residues: 411 helix: 1.44 (0.26), residues: 369 sheet: None (None), residues: 0 loop : -0.03 (0.95), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 532 TYR 0.011 0.002 TYR A 120 PHE 0.011 0.001 PHE A 327 TRP 0.034 0.002 TRP A 178 HIS 0.006 0.002 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 3299) covalent geometry : angle 0.56621 / 0.30 ( 4474) hydrogen bonds : bond 0.05336 / 3.60 ( 273) hydrogen bonds : angle 4.36383 / 3.07 ( 819) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.069 Fit side-chains REVERT: A 218 ILE cc_start: 0.8236 (mt) cc_final: 0.7935 (mp) REVERT: A 248 THR cc_start: 0.8086 (m) cc_final: 0.7807 (m) outliers start: 7 outliers final: 4 residues processed: 43 average time/residue: 0.1775 time to fit residues: 8.0844 Evaluate side-chains 40 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 485 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 chunk 11 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.169366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.147875 restraints weight = 3326.386| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.18 r_work: 0.3482 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3299 Z= 0.160 Angle : 0.560 8.052 4474 Z= 0.300 Chirality : 0.039 0.163 525 Planarity : 0.004 0.035 544 Dihedral : 14.198 156.386 472 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.37 % Allowed : 16.02 % Favored : 81.60 % 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 are not related in a simple way. whole: 1.89 (0.40), residues: 411 helix: 1.45 (0.26), residues: 369 sheet: None (None), residues: 0 loop : -0.03 (0.95), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 389 TYR 0.011 0.001 TYR A 116 PHE 0.012 0.001 PHE A 375 TRP 0.034 0.002 TRP A 178 HIS 0.005 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 ( 3299) covalent geometry : angle 0.55993 / 0.30 ( 4474) hydrogen bonds : bond 0.05282 / 3.56 ( 273) hydrogen bonds : angle 4.36519 / 3.07 ( 819) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.116 Fit side-chains REVERT: A 218 ILE cc_start: 0.8243 (mt) cc_final: 0.7946 (mp) REVERT: A 449 TYR cc_start: 0.8130 (m-10) cc_final: 0.7807 (m-80) outliers start: 8 outliers final: 4 residues processed: 42 average time/residue: 0.2299 time to fit residues: 10.2776 Evaluate side-chains 40 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 485 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 15 optimal weight: 0.0970 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 HIS A 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.170343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.148950 restraints weight = 3300.693| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.18 r_work: 0.3533 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3299 Z= 0.148 Angle : 0.544 7.835 4474 Z= 0.292 Chirality : 0.039 0.158 525 Planarity : 0.004 0.035 544 Dihedral : 13.989 156.049 472 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.08 % Allowed : 16.62 % Favored : 81.31 % 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 are not related in a simple way. whole: 2.02 (0.41), residues: 411 helix: 1.56 (0.26), residues: 368 sheet: None (None), residues: 0 loop : -0.17 (0.94), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 389 TYR 0.011 0.001 TYR A 120 PHE 0.011 0.001 PHE A 375 TRP 0.032 0.002 TRP A 178 HIS 0.006 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 3299) covalent geometry : angle 0.54447 / 0.29 ( 4474) hydrogen bonds : bond 0.05086 / 3.43 ( 273) hydrogen bonds : angle 4.32562 / 3.05 ( 819) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.106 Fit side-chains REVERT: A 218 ILE cc_start: 0.8231 (mt) cc_final: 0.7929 (mp) outliers start: 7 outliers final: 3 residues processed: 46 average time/residue: 0.2250 time to fit residues: 11.0528 Evaluate side-chains 44 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 485 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 0.0970 chunk 18 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 35 optimal weight: 0.3980 chunk 13 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.171413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.149784 restraints weight = 3337.880| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.19 r_work: 0.3498 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3299 Z= 0.144 Angle : 0.539 7.777 4474 Z= 0.289 Chirality : 0.039 0.156 525 Planarity : 0.004 0.034 544 Dihedral : 13.862 155.846 472 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.19 % Allowed : 17.51 % Favored : 81.31 % 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 are not related in a simple way. whole: 2.10 (0.41), residues: 411 helix: 1.59 (0.26), residues: 369 sheet: None (None), residues: 0 loop : -0.07 (0.95), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 389 TYR 0.011 0.001 TYR A 120 PHE 0.010 0.001 PHE A 375 TRP 0.032 0.002 TRP A 178 HIS 0.005 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 3299) covalent geometry : angle 0.53947 / 0.29 ( 4474) hydrogen bonds : bond 0.05011 / 3.38 ( 273) hydrogen bonds : angle 4.30913 / 3.04 ( 819) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1030.55 seconds wall clock time: 18 minutes 21.26 seconds (1101.26 seconds total)