Starting phenix.real_space_refine on Thu Oct 22 19:40:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11xx_76175/10_2026/11xx_76175.cif Found real_map, /net/cci-nas-00/data/ceres_data/11xx_76175/10_2026/11xx_76175.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11xx_76175/10_2026/11xx_76175.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11xx_76175/10_2026/11xx_76175.map" model { file = "/net/cci-nas-00/data/ceres_data/11xx_76175/10_2026/11xx_76175.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11xx_76175/10_2026/11xx_76175.cif" } resolution = 3.6 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= 0.005 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 19 5.16 5 C 2933 2.51 5 N 686 2.21 5 O 744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4382 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4382 Classifications: {'peptide': 553} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 531} Time building chain proxies: 0.97, per 1000 atoms: 0.22 Number of scatterers: 4382 At special positions: 0 Unit cell: (87.75, 70.85, 84.5, 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 19 16.00 O 744 8.00 N 686 7.00 C 2933 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: 0.33 Conformation dependent library (CDL) restraints added in 156.1 milliseconds 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1034 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 92.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 1 through 28 Processing helix chain 'A' and resid 28 through 37 removed outlier: 3.564A pdb=" N GLY A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 60 Proline residue: A 44 - end of helix Proline residue: A 51 - end of helix Processing helix chain 'A' and resid 62 through 77 removed outlier: 3.533A pdb=" N ILE A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 120 removed outlier: 3.704A pdb=" N SER A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Proline residue: A 110 - end of helix removed outlier: 3.681A pdb=" N ALA A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 141 removed outlier: 3.502A pdb=" N ILE A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET A 141 " --> pdb=" O ARG A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 145 through 159 Processing helix chain 'A' and resid 161 through 190 removed outlier: 4.334A pdb=" N THR A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 234 removed outlier: 4.983A pdb=" N ALA A 206 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ALA A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL A 208 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N HIS A 226 " --> pdb=" O ARG A 222 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ASN A 227 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 280 Proline residue: A 256 - end of helix removed outlier: 4.854A pdb=" N TYR A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Proline residue: A 265 - end of helix removed outlier: 5.065A pdb=" N ASN A 276 " --> pdb=" O GLN A 272 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLY A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 285 through 298 Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 308 through 328 removed outlier: 3.546A pdb=" N ALA A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Proline residue: A 320 - end of helix removed outlier: 3.832A pdb=" N GLU A 328 " --> pdb=" O LYS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 359 Proline residue: A 351 - end of helix Processing helix chain 'A' and resid 359 through 369 Processing helix chain 'A' and resid 378 through 391 Processing helix chain 'A' and resid 392 through 410 removed outlier: 3.801A pdb=" N LEU A 396 " --> pdb=" O PRO A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 439 removed outlier: 3.765A pdb=" N THR A 416 " --> pdb=" O LYS A 412 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N TYR A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) Proline residue: A 433 - end of helix Processing helix chain 'A' and resid 440 through 466 removed outlier: 4.156A pdb=" N ILE A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 502 removed outlier: 3.734A pdb=" N PHE A 481 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 500 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE A 501 " --> pdb=" O LEU A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 531 Processing helix chain 'A' and resid 533 through 537 Processing helix chain 'A' and resid 540 through 553 360 hydrogen bonds defined for protein. 1074 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: 0.61 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1295 1.34 - 1.46: 880 1.46 - 1.57: 2282 1.57 - 1.69: 0 1.69 - 1.80: 37 Bond restraints: 4494 Sorted by residual: bond pdb=" CB TRP A 152 " pdb=" CG TRP A 152 " ideal model delta sigma weight residual 1.498 1.450 0.048 3.10e-02 1.04e+03 2.39e+00 bond pdb=" CG LEU A 345 " pdb=" CD1 LEU A 345 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.06e+00 bond pdb=" CB VAL A 402 " pdb=" CG2 VAL A 402 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.75e+00 bond pdb=" CB PHE A 91 " pdb=" CG PHE A 91 " ideal model delta sigma weight residual 1.502 1.473 0.029 2.30e-02 1.89e+03 1.64e+00 bond pdb=" CG LEU A 318 " pdb=" CD2 LEU A 318 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.37e+00 ... (remaining 4489 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 5950 1.73 - 3.46: 124 3.46 - 5.20: 29 5.20 - 6.93: 8 6.93 - 8.66: 1 Bond angle restraints: 6112 Sorted by residual: angle pdb=" CA TRP A 152 " pdb=" CB TRP A 152 " pdb=" CG TRP A 152 " ideal model delta sigma weight residual 113.60 122.26 -8.66 1.90e+00 2.77e-01 2.08e+01 angle pdb=" N TRP A 152 " pdb=" CA TRP A 152 " pdb=" CB TRP A 152 " ideal model delta sigma weight residual 110.20 105.40 4.80 1.49e+00 4.50e-01 1.04e+01 angle pdb=" C TRP A 152 " pdb=" CA TRP A 152 " pdb=" CB TRP A 152 " ideal model delta sigma weight residual 110.70 115.72 -5.02 1.83e+00 2.99e-01 7.53e+00 angle pdb=" CA TYR A 87 " pdb=" CB TYR A 87 " pdb=" CG TYR A 87 " ideal model delta sigma weight residual 113.90 118.82 -4.92 1.80e+00 3.09e-01 7.46e+00 angle pdb=" C TYR A 49 " pdb=" N ALA A 50 " pdb=" CA ALA A 50 " ideal model delta sigma weight residual 120.26 116.66 3.60 1.34e+00 5.57e-01 7.22e+00 ... (remaining 6107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 2464 17.44 - 34.88: 141 34.88 - 52.33: 13 52.33 - 69.77: 4 69.77 - 87.21: 1 Dihedral angle restraints: 2623 sinusoidal: 1005 harmonic: 1618 Sorted by residual: dihedral pdb=" CA TYR A 74 " pdb=" C TYR A 74 " pdb=" N ASN A 75 " pdb=" CA ASN A 75 " ideal model delta harmonic sigma weight residual 180.00 163.13 16.87 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA TYR A 389 " pdb=" C TYR A 389 " pdb=" N TYR A 390 " pdb=" CA TYR A 390 " ideal model delta harmonic sigma weight residual -180.00 -164.21 -15.79 0 5.00e+00 4.00e-02 9.97e+00 dihedral pdb=" CA ASP A 411 " pdb=" C ASP A 411 " pdb=" N LYS A 412 " pdb=" CA LYS A 412 " ideal model delta harmonic sigma weight residual 180.00 164.56 15.44 0 5.00e+00 4.00e-02 9.53e+00 ... (remaining 2620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 439 0.036 - 0.072: 212 0.072 - 0.107: 50 0.107 - 0.143: 23 0.143 - 0.179: 1 Chirality restraints: 725 Sorted by residual: chirality pdb=" CA TYR A 49 " pdb=" N TYR A 49 " pdb=" C TYR A 49 " pdb=" CB TYR A 49 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.00e-01 chirality pdb=" CA MET A 94 " pdb=" N MET A 94 " pdb=" C MET A 94 " pdb=" CB MET A 94 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA TYR A 74 " pdb=" N TYR A 74 " pdb=" C TYR A 74 " pdb=" CB TYR A 74 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 722 not shown) Planarity restraints: 737 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 63 " -0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO A 64 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 49 " 0.020 2.00e-02 2.50e+03 1.46e-02 4.26e+00 pdb=" CG TYR A 49 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A 49 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 49 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 49 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 49 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 49 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 49 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 45 " -0.016 2.00e-02 2.50e+03 1.40e-02 3.42e+00 pdb=" CG PHE A 45 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A 45 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 45 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 45 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 45 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 45 " -0.000 2.00e-02 2.50e+03 ... (remaining 734 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 440 2.73 - 3.27: 4789 3.27 - 3.81: 7322 3.81 - 4.36: 8687 4.36 - 4.90: 14726 Nonbonded interactions: 35964 Sorted by model distance: nonbonded pdb=" OG1 THR A 11 " pdb=" OG SER A 317 " model vdw 2.187 3.040 nonbonded pdb=" NH2 ARG A 153 " pdb=" OE1 GLU A 172 " model vdw 2.230 3.120 nonbonded pdb=" OG1 THR A 274 " pdb=" ND2 ASN A 431 " model vdw 2.231 3.120 nonbonded pdb=" OD1 ASN A 227 " pdb=" NH2 ARG A 230 " model vdw 2.231 3.120 nonbonded pdb=" OH TYR A 47 " pdb=" ND2 ASN A 120 " model vdw 2.250 3.120 ... (remaining 35959 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.640 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: 0.020 Set scattering table: 0.020 Process input model: 5.340 Find NCS groups from input model: 0.020 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 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 : 0.006 0.049 4494 Z= 0.259 Angle : 0.700 8.658 6112 Z= 0.385 Chirality : 0.045 0.179 725 Planarity : 0.006 0.062 737 Dihedral : 11.042 87.208 1589 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.29), residues: 551 helix: -1.10 (0.18), residues: 478 sheet: None (None), residues: 0 loop : 1.06 (0.81), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 339 TYR 0.035 0.002 TYR A 49 PHE 0.032 0.002 PHE A 45 TRP 0.021 0.003 TRP A 152 HIS 0.003 0.001 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.26 ( 4494) covalent geometry : angle 0.70049 / 0.38 ( 6112) hydrogen bonds : bond 0.12004 / 7.26 ( 360) hydrogen bonds : angle 5.67268 / 4.19 ( 1074) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 120 ASN cc_start: 0.7233 (t0) cc_final: 0.6940 (t0) REVERT: A 264 TYR cc_start: 0.7883 (t80) cc_final: 0.7583 (t80) REVERT: A 302 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8493 (mttt) REVERT: A 367 PHE cc_start: 0.8563 (m-80) cc_final: 0.8297 (m-80) REVERT: A 470 PHE cc_start: 0.8070 (m-80) cc_final: 0.7051 (t80) REVERT: A 510 LEU cc_start: 0.9009 (tp) cc_final: 0.8805 (tp) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.0682 time to fit residues: 12.1627 Evaluate side-chains 91 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [54, 24, 48, 26, 2, 16, 32, 31, 25, 50, 53] chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.0980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN A 226 HIS A 289 GLN A 380 ASN A 476 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.135478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.104831 restraints weight = 6732.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.108643 restraints weight = 3434.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.110907 restraints weight = 2348.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.112551 restraints weight = 1903.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.113311 restraints weight = 1662.588| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4494 Z= 0.156 Angle : 0.623 6.697 6112 Z= 0.329 Chirality : 0.042 0.195 725 Planarity : 0.005 0.039 737 Dihedral : 4.042 19.248 602 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.69 % Allowed : 12.03 % Favored : 86.29 % 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: 1.45 (0.34), residues: 551 helix: 1.10 (0.22), residues: 475 sheet: None (None), residues: 0 loop : 0.68 (0.80), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 339 TYR 0.023 0.002 TYR A 87 PHE 0.029 0.002 PHE A 468 TRP 0.014 0.002 TRP A 152 HIS 0.014 0.002 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 4494) covalent geometry : angle 0.62262 / 0.33 ( 6112) hydrogen bonds : bond 0.04839 / 2.94 ( 360) hydrogen bonds : angle 4.32684 / 3.13 ( 1074) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.155 Fit side-chains REVERT: A 7 MET cc_start: 0.8186 (ttm) cc_final: 0.7957 (ttt) REVERT: A 203 THR cc_start: 0.9186 (m) cc_final: 0.8971 (m) REVERT: A 302 LYS cc_start: 0.8568 (mmtt) cc_final: 0.8229 (mttt) REVERT: A 367 PHE cc_start: 0.8508 (m-80) cc_final: 0.8222 (m-80) REVERT: A 470 PHE cc_start: 0.8180 (m-80) cc_final: 0.6971 (t80) REVERT: A 479 LYS cc_start: 0.8858 (mttt) cc_final: 0.8206 (mmtt) outliers start: 8 outliers final: 3 residues processed: 104 average time/residue: 0.0468 time to fit residues: 6.9158 Evaluate side-chains 90 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 526 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [11, 30, 14, 46, 43, 40, 51, 47, 24, 48, 38] chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 377 HIS ** A 380 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 = 0.3575 r_free = 0.3575 target = 0.133129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.102526 restraints weight = 6754.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.106238 restraints weight = 3493.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.108553 restraints weight = 2399.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.109858 restraints weight = 1937.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.110784 restraints weight = 1720.610| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4494 Z= 0.162 Angle : 0.621 8.354 6112 Z= 0.320 Chirality : 0.043 0.294 725 Planarity : 0.004 0.039 737 Dihedral : 3.993 18.395 602 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.95 % Allowed : 14.56 % Favored : 82.49 % 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: 2.21 (0.36), residues: 551 helix: 1.65 (0.24), residues: 475 sheet: None (None), residues: 0 loop : 0.59 (0.81), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 339 TYR 0.021 0.002 TYR A 87 PHE 0.018 0.002 PHE A 468 TRP 0.011 0.002 TRP A 152 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 ( 4494) covalent geometry : angle 0.62093 / 0.32 ( 6112) hydrogen bonds : bond 0.04350 / 2.66 ( 360) hydrogen bonds : angle 4.07806 / 2.91 ( 1074) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.148 Fit side-chains REVERT: A 302 LYS cc_start: 0.8611 (mmtt) cc_final: 0.8217 (mttt) REVERT: A 367 PHE cc_start: 0.8535 (m-80) cc_final: 0.8254 (m-80) REVERT: A 470 PHE cc_start: 0.8241 (m-80) cc_final: 0.6897 (t80) REVERT: A 479 LYS cc_start: 0.8801 (mttt) cc_final: 0.8208 (mmtt) outliers start: 14 outliers final: 7 residues processed: 98 average time/residue: 0.0424 time to fit residues: 5.9336 Evaluate side-chains 90 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 526 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [24, 38, 17, 37, 9, 40, 8, 1, 4, 11, 2] chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.132718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.102022 restraints weight = 6668.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.105682 restraints weight = 3498.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.108031 restraints weight = 2421.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.109460 restraints weight = 1950.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.110170 restraints weight = 1717.512| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4494 Z= 0.170 Angle : 0.610 7.047 6112 Z= 0.315 Chirality : 0.042 0.163 725 Planarity : 0.004 0.042 737 Dihedral : 3.925 17.377 602 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.38 % Allowed : 16.24 % Favored : 80.38 % 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: 2.48 (0.36), residues: 551 helix: 1.87 (0.24), residues: 475 sheet: None (None), residues: 0 loop : 0.40 (0.81), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 339 TYR 0.020 0.001 TYR A 87 PHE 0.027 0.002 PHE A 495 TRP 0.011 0.002 TRP A 152 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 ( 4494) covalent geometry : angle 0.60957 / 0.32 ( 6112) hydrogen bonds : bond 0.04178 / 2.55 ( 360) hydrogen bonds : angle 3.99809 / 2.88 ( 1074) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.162 Fit side-chains REVERT: A 302 LYS cc_start: 0.8616 (mmtt) cc_final: 0.8194 (mttt) REVERT: A 367 PHE cc_start: 0.8559 (m-80) cc_final: 0.8290 (m-80) REVERT: A 470 PHE cc_start: 0.8286 (m-80) cc_final: 0.6907 (t80) REVERT: A 479 LYS cc_start: 0.8811 (mttt) cc_final: 0.8196 (mmtt) outliers start: 16 outliers final: 8 residues processed: 100 average time/residue: 0.0440 time to fit residues: 6.2909 Evaluate side-chains 93 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 526 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [7, 52, 51, 1, 0, 41, 38, 5, 17, 47, 27] chunk 7 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 5 optimal weight: 0.2980 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.134620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.102480 restraints weight = 6951.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.106294 restraints weight = 3498.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.108736 restraints weight = 2376.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.109919 restraints weight = 1911.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.111056 restraints weight = 1708.767| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 4494 Z= 0.155 Angle : 0.602 6.770 6112 Z= 0.313 Chirality : 0.041 0.156 725 Planarity : 0.004 0.042 737 Dihedral : 3.880 18.205 602 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.95 % Allowed : 16.46 % Favored : 80.59 % 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: 2.64 (0.36), residues: 551 helix: 1.99 (0.24), residues: 475 sheet: None (None), residues: 0 loop : 0.38 (0.80), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 339 TYR 0.027 0.001 TYR A 368 PHE 0.015 0.001 PHE A 496 TRP 0.011 0.002 TRP A 152 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 4494) covalent geometry : angle 0.60205 / 0.31 ( 6112) hydrogen bonds : bond 0.04051 / 2.46 ( 360) hydrogen bonds : angle 3.93819 / 2.84 ( 1074) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.177 Fit side-chains REVERT: A 302 LYS cc_start: 0.8642 (mmtt) cc_final: 0.8353 (mttt) REVERT: A 367 PHE cc_start: 0.8604 (m-80) cc_final: 0.8357 (m-80) REVERT: A 470 PHE cc_start: 0.8288 (m-80) cc_final: 0.6924 (t80) REVERT: A 479 LYS cc_start: 0.8805 (mttt) cc_final: 0.8284 (mttt) outliers start: 14 outliers final: 11 residues processed: 98 average time/residue: 0.0461 time to fit residues: 6.4343 Evaluate side-chains 95 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 526 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [20, 16, 2, 6, 1, 48, 21, 30, 40, 28, 11] chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 0.0370 chunk 6 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.135470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.103373 restraints weight = 7018.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.107255 restraints weight = 3492.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.109720 restraints weight = 2366.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.110939 restraints weight = 1899.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.111982 restraints weight = 1693.417| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4494 Z= 0.146 Angle : 0.604 11.623 6112 Z= 0.313 Chirality : 0.041 0.155 725 Planarity : 0.004 0.042 737 Dihedral : 3.834 17.242 602 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.80 % Allowed : 16.24 % Favored : 79.96 % 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: 2.75 (0.36), residues: 551 helix: 2.07 (0.24), residues: 476 sheet: None (None), residues: 0 loop : 0.38 (0.80), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 339 TYR 0.025 0.001 TYR A 368 PHE 0.030 0.001 PHE A 495 TRP 0.010 0.002 TRP A 152 HIS 0.001 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 4494) covalent geometry : angle 0.60397 / 0.31 ( 6112) hydrogen bonds : bond 0.03958 / 2.41 ( 360) hydrogen bonds : angle 3.92771 / 2.84 ( 1074) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: A 162 MET cc_start: 0.8038 (mmt) cc_final: 0.7721 (mmt) REVERT: A 248 LYS cc_start: 0.8400 (tttt) cc_final: 0.7918 (mtpt) REVERT: A 302 LYS cc_start: 0.8662 (mmtt) cc_final: 0.8430 (mttt) REVERT: A 367 PHE cc_start: 0.8627 (m-80) cc_final: 0.8404 (m-80) REVERT: A 470 PHE cc_start: 0.8261 (m-80) cc_final: 0.6912 (t80) outliers start: 18 outliers final: 13 residues processed: 100 average time/residue: 0.0476 time to fit residues: 6.7166 Evaluate side-chains 97 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 526 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [45, 17, 10, 18, 33, 13, 35, 51, 12, 31, 7] chunk 45 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 35 optimal weight: 0.0370 chunk 51 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.133532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.102621 restraints weight = 6833.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.106406 restraints weight = 3398.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.108810 restraints weight = 2286.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.110010 restraints weight = 1822.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.111151 restraints weight = 1621.209| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4494 Z= 0.151 Angle : 0.611 11.152 6112 Z= 0.316 Chirality : 0.041 0.175 725 Planarity : 0.004 0.042 737 Dihedral : 3.840 16.429 602 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.59 % Allowed : 17.51 % Favored : 78.90 % 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: 2.75 (0.36), residues: 551 helix: 2.07 (0.24), residues: 476 sheet: None (None), residues: 0 loop : 0.34 (0.80), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 339 TYR 0.023 0.001 TYR A 368 PHE 0.020 0.001 PHE A 496 TRP 0.010 0.002 TRP A 152 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 ( 4494) covalent geometry : angle 0.61134 / 0.32 ( 6112) hydrogen bonds : bond 0.03956 / 2.41 ( 360) hydrogen bonds : angle 3.92574 / 2.84 ( 1074) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.127 Fit side-chains REVERT: A 162 MET cc_start: 0.8029 (mmt) cc_final: 0.7736 (mmt) REVERT: A 248 LYS cc_start: 0.8394 (tttt) cc_final: 0.7905 (mtpt) REVERT: A 302 LYS cc_start: 0.8679 (mmtt) cc_final: 0.8355 (mttt) REVERT: A 367 PHE cc_start: 0.8637 (m-80) cc_final: 0.8418 (m-80) REVERT: A 470 PHE cc_start: 0.8266 (m-80) cc_final: 0.6903 (t80) REVERT: A 479 LYS cc_start: 0.8790 (mttt) cc_final: 0.8274 (mttt) outliers start: 17 outliers final: 13 residues processed: 98 average time/residue: 0.0465 time to fit residues: 6.3663 Evaluate side-chains 97 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 526 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [45, 44, 43, 7, 27, 0, 32, 46, 28, 29, 23] chunk 45 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 43 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.133555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.102603 restraints weight = 6876.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.106361 restraints weight = 3416.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.108791 restraints weight = 2313.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.110036 restraints weight = 1846.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.111212 restraints weight = 1638.550| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 4494 Z= 0.158 Angle : 0.623 9.982 6112 Z= 0.322 Chirality : 0.041 0.162 725 Planarity : 0.004 0.043 737 Dihedral : 3.836 16.000 602 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.59 % Allowed : 18.14 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.36), residues: 551 helix: 2.04 (0.24), residues: 476 sheet: None (None), residues: 0 loop : 0.31 (0.80), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 546 TYR 0.022 0.001 TYR A 368 PHE 0.017 0.001 PHE A 496 TRP 0.010 0.002 TRP A 152 HIS 0.003 0.001 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 ( 4494) covalent geometry : angle 0.62291 / 0.32 ( 6112) hydrogen bonds : bond 0.03985 / 2.46 ( 360) hydrogen bonds : angle 3.97197 / 2.87 ( 1074) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: A 162 MET cc_start: 0.8028 (mmt) cc_final: 0.7758 (mmt) REVERT: A 248 LYS cc_start: 0.8385 (tttt) cc_final: 0.7902 (mtpt) REVERT: A 302 LYS cc_start: 0.8691 (mmtt) cc_final: 0.8383 (mttt) REVERT: A 367 PHE cc_start: 0.8651 (m-80) cc_final: 0.8426 (m-80) REVERT: A 470 PHE cc_start: 0.8253 (m-80) cc_final: 0.6879 (t80) outliers start: 17 outliers final: 13 residues processed: 101 average time/residue: 0.0435 time to fit residues: 6.2096 Evaluate side-chains 98 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 526 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [47, 32, 31, 51, 23, 5, 26, 13, 54, 52, 19] chunk 47 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 54 optimal weight: 0.4980 chunk 52 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 GLN ** A 431 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 = 0.3602 r_free = 0.3602 target = 0.134821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.102627 restraints weight = 6976.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.106489 restraints weight = 3551.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.108922 restraints weight = 2421.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.110367 restraints weight = 1942.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.110913 restraints weight = 1711.397| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 4494 Z= 0.162 Angle : 0.610 8.350 6112 Z= 0.320 Chirality : 0.041 0.211 725 Planarity : 0.004 0.043 737 Dihedral : 3.837 17.284 602 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.38 % Allowed : 17.51 % Favored : 79.11 % 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: 2.73 (0.36), residues: 551 helix: 2.06 (0.24), residues: 477 sheet: None (None), residues: 0 loop : 0.25 (0.81), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 339 TYR 0.021 0.001 TYR A 368 PHE 0.018 0.001 PHE A 496 TRP 0.021 0.002 TRP A 152 HIS 0.002 0.001 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.16 ( 4494) covalent geometry : angle 0.60997 / 0.32 ( 6112) hydrogen bonds : bond 0.04013 / 2.44 ( 360) hydrogen bonds : angle 3.97944 / 2.88 ( 1074) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: A 162 MET cc_start: 0.8024 (mmt) cc_final: 0.7756 (mmt) REVERT: A 248 LYS cc_start: 0.8391 (tttt) cc_final: 0.7902 (mtpt) REVERT: A 302 LYS cc_start: 0.8708 (mmtt) cc_final: 0.8369 (mttt) REVERT: A 367 PHE cc_start: 0.8667 (m-80) cc_final: 0.8442 (m-80) outliers start: 16 outliers final: 15 residues processed: 96 average time/residue: 0.0411 time to fit residues: 5.5775 Evaluate side-chains 100 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 526 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [51, 39, 53, 22, 3, 5, 16, 45, 33, 12, 29] chunk 51 optimal weight: 0.9990 chunk 39 optimal weight: 0.0770 chunk 53 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.135652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.103534 restraints weight = 6993.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.107286 restraints weight = 3629.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.109667 restraints weight = 2491.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.111057 restraints weight = 2014.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.111782 restraints weight = 1784.502| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 4494 Z= 0.157 Angle : 0.607 7.376 6112 Z= 0.321 Chirality : 0.041 0.218 725 Planarity : 0.004 0.043 737 Dihedral : 3.839 20.776 602 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.59 % Allowed : 17.72 % Favored : 78.69 % 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: 2.80 (0.36), residues: 551 helix: 2.12 (0.24), residues: 477 sheet: None (None), residues: 0 loop : 0.19 (0.81), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 339 TYR 0.027 0.001 TYR A 52 PHE 0.018 0.001 PHE A 496 TRP 0.018 0.002 TRP A 152 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 4494) covalent geometry : angle 0.60748 / 0.32 ( 6112) hydrogen bonds : bond 0.03997 / 2.42 ( 360) hydrogen bonds : angle 3.97312 / 2.88 ( 1074) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 162 MET cc_start: 0.8014 (mmt) cc_final: 0.7734 (mmt) REVERT: A 248 LYS cc_start: 0.8396 (tttt) cc_final: 0.7913 (mtpt) REVERT: A 302 LYS cc_start: 0.8700 (mmtt) cc_final: 0.8382 (mttt) REVERT: A 367 PHE cc_start: 0.8664 (m-80) cc_final: 0.8423 (m-80) REVERT: A 368 TYR cc_start: 0.8155 (m-10) cc_final: 0.7780 (m-10) outliers start: 17 outliers final: 12 residues processed: 101 average time/residue: 0.0486 time to fit residues: 6.7715 Evaluate side-chains 97 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 526 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: [29, 41, 49, 31, 9, 46, 7, 10, 43, 50, 47] chunk 29 optimal weight: 0.8980 chunk 41 optimal weight: 0.2980 chunk 49 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 50 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.140223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.107597 restraints weight = 6957.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.111352 restraints weight = 3631.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.113660 restraints weight = 2523.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.115234 restraints weight = 2060.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.115705 restraints weight = 1819.638| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 4494 Z= 0.151 Angle : 0.609 9.024 6112 Z= 0.320 Chirality : 0.041 0.196 725 Planarity : 0.004 0.042 737 Dihedral : 3.792 17.228 602 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.74 % Allowed : 19.41 % Favored : 77.85 % 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: 2.84 (0.36), residues: 551 helix: 2.15 (0.24), residues: 475 sheet: None (None), residues: 0 loop : 0.22 (0.79), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 339 TYR 0.020 0.001 TYR A 368 PHE 0.033 0.001 PHE A 496 TRP 0.015 0.002 TRP A 152 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 4494) covalent geometry : angle 0.60866 / 0.32 ( 6112) hydrogen bonds : bond 0.03979 / 2.40 ( 360) hydrogen bonds : angle 3.95652 / 2.87 ( 1074) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 929.28 seconds wall clock time: 16 minutes 38.44 seconds (998.44 seconds total)