Starting phenix.real_space_refine on Tue Mar 3 11:24:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cyh_30500/03_2026/7cyh_30500.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cyh_30500/03_2026/7cyh_30500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7cyh_30500/03_2026/7cyh_30500.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cyh_30500/03_2026/7cyh_30500.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cyh_30500/03_2026/7cyh_30500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cyh_30500/03_2026/7cyh_30500.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.210 sd= 1.412 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 14 5.16 5 C 2057 2.51 5 N 551 2.21 5 O 619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3241 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "D" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 806 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 899 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 0.81, per 1000 atoms: 0.25 Number of scatterers: 3241 At special positions: 0 Unit cell: (72.45, 61.95, 92.4, 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 14 16.00 O 619 8.00 N 551 7.00 C 2057 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 91 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 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: 0.27 Conformation dependent library (CDL) restraints added in 111.3 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 11 sheets defined 9.5% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.554A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.911A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.841A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'E' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.024A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 400 through 403 removed outlier: 3.650A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A 434 " --> pdb=" O VAL A 511 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.885A pdb=" N CYS D 22 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER D 70 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 39 through 41 removed outlier: 4.021A pdb=" N VAL D 88 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.785A pdb=" N LYS E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AB1, first strand: chain 'E' and resid 45 through 50 removed outlier: 6.383A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLU E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N MET E 34 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N CYS E 96 " --> pdb=" O TRP E 110 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TRP E 110 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ARG E 98 " --> pdb=" O ASP E 108 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 45 through 50 removed outlier: 6.383A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLU E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N MET E 34 " --> pdb=" O GLU E 50 " (cutoff:3.500A) 71 hydrogen bonds defined for protein. 156 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: 0.49 Time building geometry restraints manager: 0.36 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: 1045 1.34 - 1.46: 891 1.46 - 1.59: 1370 1.59 - 1.71: 0 1.71 - 1.83: 16 Bond restraints: 3322 Sorted by residual: bond pdb=" C PHE A 497 " pdb=" N GLN A 498 " ideal model delta sigma weight residual 1.329 1.256 0.073 1.86e-02 2.89e+03 1.53e+01 bond pdb=" CA VAL A 512 " pdb=" C VAL A 512 " ideal model delta sigma weight residual 1.525 1.503 0.022 9.00e-03 1.23e+04 6.10e+00 bond pdb=" C GLN A 498 " pdb=" N PRO A 499 " ideal model delta sigma weight residual 1.336 1.307 0.029 1.25e-02 6.40e+03 5.50e+00 bond pdb=" CB PHE A 429 " pdb=" CG PHE A 429 " ideal model delta sigma weight residual 1.502 1.449 0.053 2.30e-02 1.89e+03 5.27e+00 bond pdb=" CB PHE A 377 " pdb=" CG PHE A 377 " ideal model delta sigma weight residual 1.502 1.449 0.053 2.30e-02 1.89e+03 5.24e+00 ... (remaining 3317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 4410 3.27 - 6.55: 95 6.55 - 9.82: 9 9.82 - 13.09: 0 13.09 - 16.36: 1 Bond angle restraints: 4515 Sorted by residual: angle pdb=" C PHE A 497 " pdb=" N GLN A 498 " pdb=" CA GLN A 498 " ideal model delta sigma weight residual 121.48 105.12 16.36 2.04e+00 2.40e-01 6.44e+01 angle pdb=" N VAL A 512 " pdb=" CA VAL A 512 " pdb=" C VAL A 512 " ideal model delta sigma weight residual 108.53 99.98 8.55 1.22e+00 6.72e-01 4.91e+01 angle pdb=" N GLY E 105 " pdb=" CA GLY E 105 " pdb=" C GLY E 105 " ideal model delta sigma weight residual 111.42 103.58 7.84 1.51e+00 4.39e-01 2.69e+01 angle pdb=" C PHE D 35 " pdb=" N MET D 36 " pdb=" CA MET D 36 " ideal model delta sigma weight residual 121.53 131.27 -9.74 2.25e+00 1.98e-01 1.87e+01 angle pdb=" C ARG D 99 " pdb=" N ILE D 100 " pdb=" CA ILE D 100 " ideal model delta sigma weight residual 121.97 128.15 -6.18 1.80e+00 3.09e-01 1.18e+01 ... (remaining 4510 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 15.72: 1830 15.72 - 31.43: 108 31.43 - 47.14: 7 47.14 - 62.85: 1 62.85 - 78.56: 1 Dihedral angle restraints: 1947 sinusoidal: 738 harmonic: 1209 Sorted by residual: dihedral pdb=" CA THR E 63 " pdb=" C THR E 63 " pdb=" N VAL E 64 " pdb=" CA VAL E 64 " ideal model delta harmonic sigma weight residual 180.00 146.98 33.02 0 5.00e+00 4.00e-02 4.36e+01 dihedral pdb=" CA GLN D 92 " pdb=" C GLN D 92 " pdb=" N GLN D 93 " pdb=" CA GLN D 93 " ideal model delta harmonic sigma weight residual 180.00 149.00 31.00 0 5.00e+00 4.00e-02 3.84e+01 dihedral pdb=" CA SER A 383 " pdb=" C SER A 383 " pdb=" N PRO A 384 " pdb=" CA PRO A 384 " ideal model delta harmonic sigma weight residual 180.00 -149.34 -30.66 0 5.00e+00 4.00e-02 3.76e+01 ... (remaining 1944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 263 0.042 - 0.084: 136 0.084 - 0.127: 55 0.127 - 0.169: 27 0.169 - 0.211: 3 Chirality restraints: 484 Sorted by residual: chirality pdb=" CA HIS A 519 " pdb=" N HIS A 519 " pdb=" C HIS A 519 " pdb=" CB HIS A 519 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL A 511 " pdb=" CA VAL A 511 " pdb=" CG1 VAL A 511 " pdb=" CG2 VAL A 511 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" CA THR E 58 " pdb=" N THR E 58 " pdb=" C THR E 58 " pdb=" CB THR E 58 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.42e-01 ... (remaining 481 not shown) Planarity restraints: 589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " 0.056 5.00e-02 4.00e+02 8.50e-02 1.16e+01 pdb=" N PRO A 527 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 398 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.31e+00 pdb=" C ASP A 398 " 0.053 2.00e-02 2.50e+03 pdb=" O ASP A 398 " -0.020 2.00e-02 2.50e+03 pdb=" N SER A 399 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR E 60 " -0.037 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO E 61 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO E 61 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 61 " -0.030 5.00e-02 4.00e+02 ... (remaining 586 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 107 2.65 - 3.21: 3284 3.21 - 3.77: 4889 3.77 - 4.34: 6489 4.34 - 4.90: 10557 Nonbonded interactions: 25326 Sorted by model distance: nonbonded pdb=" OG1 THR A 393 " pdb=" OE1 GLU A 516 " model vdw 2.087 3.040 nonbonded pdb=" O THR E 30 " pdb=" OG SER E 53 " model vdw 2.093 3.040 nonbonded pdb=" O SER E 52 " pdb=" NH1 ARG E 72 " model vdw 2.145 3.120 nonbonded pdb=" O LEU A 513 " pdb=" OG SER A 514 " model vdw 2.165 3.040 nonbonded pdb=" NH1 ARG A 457 " pdb=" OG SER A 459 " model vdw 2.169 3.120 ... (remaining 25321 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.460 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.500 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6059 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 : 0.011 0.073 3327 Z= 0.494 Angle : 1.177 16.365 4525 Z= 0.656 Chirality : 0.062 0.211 484 Planarity : 0.008 0.085 589 Dihedral : 9.756 78.558 1170 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 28.64 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.83 % Favored : 89.69 % Rotamer: Outliers : 0.87 % Allowed : 0.87 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % Twisted Proline : 4.76 % Twisted General : 0.75 % 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: -4.10 (0.33), residues: 417 helix: -4.58 (0.31), residues: 26 sheet: -2.91 (0.39), residues: 108 loop : -2.59 (0.31), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 466 TYR 0.032 0.004 TYR A 495 PHE 0.036 0.005 PHE A 497 TRP 0.021 0.004 TRP A 353 HIS 0.000 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.01073 ( 3322) covalent geometry : angle 1.17561 ( 4515) SS BOND : bond 0.00608 ( 5) SS BOND : angle 1.71565 ( 10) hydrogen bonds : bond 0.31241 ( 62) hydrogen bonds : angle 12.73712 ( 156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8298 (m-80) cc_final: 0.8049 (m-80) REVERT: A 493 GLN cc_start: 0.7362 (tt0) cc_final: 0.7029 (tt0) outliers start: 3 outliers final: 3 residues processed: 112 average time/residue: 0.0846 time to fit residues: 10.9159 Evaluate side-chains 73 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 515 PHE 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: 7.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN D 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.158097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.111596 restraints weight = 5457.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.113978 restraints weight = 3681.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.115735 restraints weight = 2856.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.116540 restraints weight = 2433.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.117269 restraints weight = 2211.438| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 3327 Z= 0.248 Angle : 0.876 8.942 4525 Z= 0.462 Chirality : 0.053 0.170 484 Planarity : 0.007 0.050 589 Dihedral : 8.649 59.097 474 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.11 % Favored : 90.41 % Rotamer: Outliers : 4.07 % Allowed : 9.01 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: -3.09 (0.37), residues: 417 helix: -4.12 (0.56), residues: 25 sheet: -2.38 (0.46), residues: 95 loop : -1.84 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 357 TYR 0.030 0.003 TYR A 495 PHE 0.028 0.003 PHE A 497 TRP 0.020 0.002 TRP A 353 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00558 ( 3322) covalent geometry : angle 0.87525 ( 4515) SS BOND : bond 0.00582 ( 5) SS BOND : angle 1.31516 ( 10) hydrogen bonds : bond 0.04758 ( 62) hydrogen bonds : angle 9.83098 ( 156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.8131 (ttt90) cc_final: 0.7755 (ttt90) REVERT: A 493 GLN cc_start: 0.7425 (tt0) cc_final: 0.7086 (tt0) REVERT: D 56 ASN cc_start: 0.7433 (m110) cc_final: 0.7033 (m110) REVERT: E 34 MET cc_start: 0.7681 (mmm) cc_final: 0.7338 (mmm) outliers start: 14 outliers final: 9 residues processed: 97 average time/residue: 0.0680 time to fit residues: 7.7781 Evaluate side-chains 82 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain E residue 96 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 24 optimal weight: 0.0870 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 GLN ** 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 = 0.4270 r_free = 0.4270 target = 0.160485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.114714 restraints weight = 5318.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.116977 restraints weight = 3990.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.117912 restraints weight = 2992.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.118060 restraints weight = 2665.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.118252 restraints weight = 2706.544| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 3327 Z= 0.192 Angle : 0.846 12.953 4525 Z= 0.430 Chirality : 0.051 0.211 484 Planarity : 0.006 0.060 589 Dihedral : 7.705 50.030 474 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.39 % Favored : 91.13 % Rotamer: Outliers : 4.65 % Allowed : 13.95 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: -2.55 (0.39), residues: 417 helix: -3.88 (0.67), residues: 25 sheet: -1.93 (0.47), residues: 103 loop : -1.44 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 454 TYR 0.030 0.002 TYR D 52 PHE 0.024 0.003 PHE D 101 TRP 0.016 0.002 TRP A 353 HIS 0.004 0.003 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 3322) covalent geometry : angle 0.84178 ( 4515) SS BOND : bond 0.01537 ( 5) SS BOND : angle 1.90692 ( 10) hydrogen bonds : bond 0.03858 ( 62) hydrogen bonds : angle 8.75355 ( 156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.8091 (ttt90) cc_final: 0.7758 (ttt90) REVERT: A 406 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7355 (mt-10) REVERT: D 101 PHE cc_start: 0.8910 (m-80) cc_final: 0.8660 (m-10) REVERT: E 34 MET cc_start: 0.7651 (mmm) cc_final: 0.7445 (mmm) REVERT: E 80 TYR cc_start: 0.8796 (m-80) cc_final: 0.8174 (m-10) outliers start: 16 outliers final: 11 residues processed: 98 average time/residue: 0.0755 time to fit residues: 8.8624 Evaluate side-chains 85 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN D 40 GLN D 45 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.163633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.118307 restraints weight = 5285.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.121127 restraints weight = 3483.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.123195 restraints weight = 2668.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.124578 restraints weight = 2228.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.125191 restraints weight = 1979.325| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 3327 Z= 0.141 Angle : 0.753 10.448 4525 Z= 0.385 Chirality : 0.049 0.199 484 Planarity : 0.005 0.064 589 Dihedral : 6.688 38.112 473 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.95 % Favored : 92.57 % Rotamer: Outliers : 4.94 % Allowed : 15.99 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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 (0.40), residues: 417 helix: -3.90 (0.60), residues: 25 sheet: -1.69 (0.48), residues: 104 loop : -1.17 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 454 TYR 0.031 0.002 TYR D 52 PHE 0.019 0.002 PHE A 429 TRP 0.023 0.002 TRP E 47 HIS 0.003 0.002 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 3322) covalent geometry : angle 0.74988 ( 4515) SS BOND : bond 0.00874 ( 5) SS BOND : angle 1.71095 ( 10) hydrogen bonds : bond 0.03212 ( 62) hydrogen bonds : angle 7.93964 ( 156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.7992 (ttt90) cc_final: 0.7602 (ttt90) REVERT: A 376 THR cc_start: 0.8674 (t) cc_final: 0.8409 (p) REVERT: A 389 ASP cc_start: 0.7426 (t70) cc_final: 0.6893 (t0) REVERT: D 37 ASN cc_start: 0.6572 (m110) cc_final: 0.6206 (m-40) outliers start: 17 outliers final: 12 residues processed: 99 average time/residue: 0.0743 time to fit residues: 8.7015 Evaluate side-chains 85 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 23 optimal weight: 0.5980 chunk 32 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN ** D 45 GLN ** 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 = 0.4252 r_free = 0.4252 target = 0.158799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.112725 restraints weight = 5245.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.115282 restraints weight = 3491.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.117104 restraints weight = 2679.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.118121 restraints weight = 2269.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.118538 restraints weight = 2053.265| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 3327 Z= 0.203 Angle : 0.811 10.854 4525 Z= 0.418 Chirality : 0.050 0.233 484 Planarity : 0.005 0.064 589 Dihedral : 6.574 26.483 471 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.87 % Favored : 90.65 % Rotamer: Outliers : 6.10 % Allowed : 16.86 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: -2.09 (0.42), residues: 417 helix: -4.38 (0.39), residues: 19 sheet: -1.54 (0.49), residues: 104 loop : -1.14 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 48 TYR 0.019 0.002 TYR A 495 PHE 0.020 0.003 PHE A 429 TRP 0.018 0.002 TRP E 47 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 3322) covalent geometry : angle 0.80669 ( 4515) SS BOND : bond 0.00913 ( 5) SS BOND : angle 1.99178 ( 10) hydrogen bonds : bond 0.03534 ( 62) hydrogen bonds : angle 7.81167 ( 156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 THR cc_start: 0.8747 (t) cc_final: 0.8380 (p) REVERT: A 389 ASP cc_start: 0.7217 (t70) cc_final: 0.6668 (t0) outliers start: 21 outliers final: 15 residues processed: 89 average time/residue: 0.0712 time to fit residues: 7.6193 Evaluate side-chains 74 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 0.0670 chunk 6 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 23 optimal weight: 0.4980 overall best weight: 1.0520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.163560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.118607 restraints weight = 5277.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.121653 restraints weight = 3314.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.123823 restraints weight = 2476.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.124799 restraints weight = 2043.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.126131 restraints weight = 1839.576| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.5425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3327 Z= 0.129 Angle : 0.745 8.207 4525 Z= 0.378 Chirality : 0.049 0.228 484 Planarity : 0.005 0.066 589 Dihedral : 6.009 26.649 471 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.19 % Favored : 92.33 % Rotamer: Outliers : 4.36 % Allowed : 19.48 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: -2.05 (0.41), residues: 417 helix: -4.33 (0.44), residues: 19 sheet: -1.50 (0.47), residues: 114 loop : -1.08 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 48 TYR 0.030 0.002 TYR D 52 PHE 0.016 0.002 PHE A 429 TRP 0.022 0.002 TRP E 47 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 3322) covalent geometry : angle 0.74172 ( 4515) SS BOND : bond 0.00804 ( 5) SS BOND : angle 1.69284 ( 10) hydrogen bonds : bond 0.03141 ( 62) hydrogen bonds : angle 7.04442 ( 156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 SER cc_start: 0.8150 (m) cc_final: 0.7702 (p) REVERT: A 376 THR cc_start: 0.8638 (t) cc_final: 0.8428 (p) REVERT: A 389 ASP cc_start: 0.7246 (t70) cc_final: 0.6724 (t0) REVERT: E 34 MET cc_start: 0.7792 (mmm) cc_final: 0.7545 (mmm) outliers start: 15 outliers final: 10 residues processed: 82 average time/residue: 0.0694 time to fit residues: 6.8666 Evaluate side-chains 76 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 chunk 21 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.161314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.115587 restraints weight = 5344.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.118568 restraints weight = 3413.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.120590 restraints weight = 2531.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.121673 restraints weight = 2115.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.122677 restraints weight = 1899.844| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.5574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3327 Z= 0.168 Angle : 0.771 9.082 4525 Z= 0.393 Chirality : 0.051 0.300 484 Planarity : 0.005 0.066 589 Dihedral : 6.072 27.354 471 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.72 % Allowed : 7.19 % Favored : 92.09 % Rotamer: Outliers : 5.81 % Allowed : 18.90 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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 (0.41), residues: 417 helix: -4.22 (0.44), residues: 19 sheet: -1.19 (0.49), residues: 108 loop : -1.10 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 48 TYR 0.016 0.002 TYR A 495 PHE 0.016 0.002 PHE A 429 TRP 0.021 0.002 TRP E 47 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 3322) covalent geometry : angle 0.76753 ( 4515) SS BOND : bond 0.00818 ( 5) SS BOND : angle 1.80322 ( 10) hydrogen bonds : bond 0.03259 ( 62) hydrogen bonds : angle 6.99212 ( 156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 SER cc_start: 0.8401 (m) cc_final: 0.7964 (p) REVERT: A 376 THR cc_start: 0.8728 (t) cc_final: 0.8379 (p) REVERT: A 389 ASP cc_start: 0.7272 (t70) cc_final: 0.6754 (t0) REVERT: E 34 MET cc_start: 0.7723 (mmm) cc_final: 0.7462 (mmm) outliers start: 20 outliers final: 13 residues processed: 79 average time/residue: 0.0695 time to fit residues: 6.6255 Evaluate side-chains 73 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 8.9990 chunk 31 optimal weight: 0.0870 chunk 32 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 overall best weight: 2.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN D 45 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.159345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.113613 restraints weight = 5533.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.116547 restraints weight = 3933.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.117952 restraints weight = 2674.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.118095 restraints weight = 2336.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.118323 restraints weight = 2326.746| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.5584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 3327 Z= 0.203 Angle : 0.798 9.615 4525 Z= 0.411 Chirality : 0.051 0.242 484 Planarity : 0.005 0.064 589 Dihedral : 6.268 25.487 471 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.72 % Allowed : 7.91 % Favored : 91.37 % Rotamer: Outliers : 5.81 % Allowed : 18.90 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: -1.95 (0.42), residues: 417 helix: -4.19 (0.43), residues: 19 sheet: -1.51 (0.48), residues: 111 loop : -0.99 (0.39), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 48 TYR 0.016 0.002 TYR A 495 PHE 0.018 0.003 PHE A 347 TRP 0.020 0.002 TRP E 47 HIS 0.000 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 3322) covalent geometry : angle 0.79318 ( 4515) SS BOND : bond 0.00837 ( 5) SS BOND : angle 1.95536 ( 10) hydrogen bonds : bond 0.03168 ( 62) hydrogen bonds : angle 7.16963 ( 156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 SER cc_start: 0.8476 (m) cc_final: 0.8038 (p) REVERT: A 376 THR cc_start: 0.8853 (t) cc_final: 0.8441 (m) REVERT: A 389 ASP cc_start: 0.7291 (t70) cc_final: 0.6726 (t0) REVERT: E 34 MET cc_start: 0.7687 (mmm) cc_final: 0.7423 (mmm) outliers start: 20 outliers final: 16 residues processed: 80 average time/residue: 0.0719 time to fit residues: 6.8907 Evaluate side-chains 79 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 chunk 39 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN D 37 ASN D 45 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.163713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.119810 restraints weight = 5500.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.122800 restraints weight = 3896.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.124575 restraints weight = 2546.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.124715 restraints weight = 2205.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.124936 restraints weight = 2220.261| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.5908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3327 Z= 0.132 Angle : 0.757 8.568 4525 Z= 0.382 Chirality : 0.049 0.198 484 Planarity : 0.005 0.064 589 Dihedral : 5.865 25.622 471 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.96 % Allowed : 6.95 % Favored : 92.09 % Rotamer: Outliers : 5.23 % Allowed : 19.19 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: -1.79 (0.43), residues: 417 helix: -4.19 (0.50), residues: 19 sheet: -1.23 (0.50), residues: 114 loop : -0.94 (0.40), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 48 TYR 0.023 0.002 TYR E 80 PHE 0.015 0.002 PHE D 65 TRP 0.021 0.002 TRP E 47 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 3322) covalent geometry : angle 0.75416 ( 4515) SS BOND : bond 0.00868 ( 5) SS BOND : angle 1.67816 ( 10) hydrogen bonds : bond 0.03092 ( 62) hydrogen bonds : angle 6.77042 ( 156) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 SER cc_start: 0.8195 (m) cc_final: 0.7775 (p) REVERT: A 376 THR cc_start: 0.8869 (t) cc_final: 0.8612 (p) REVERT: A 389 ASP cc_start: 0.7349 (t70) cc_final: 0.6838 (t0) REVERT: A 452 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8240 (mt) REVERT: E 11 LEU cc_start: 0.7964 (tp) cc_final: 0.7140 (mp) REVERT: E 73 ASP cc_start: 0.8344 (t0) cc_final: 0.8142 (t70) outliers start: 18 outliers final: 15 residues processed: 81 average time/residue: 0.0704 time to fit residues: 6.8916 Evaluate side-chains 82 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 45 GLN Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 39 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.162935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.119871 restraints weight = 5323.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.122484 restraints weight = 3564.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.123621 restraints weight = 2530.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.123784 restraints weight = 2247.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.124067 restraints weight = 2219.146| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.6032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 3327 Z= 0.221 Angle : 1.405 59.139 4525 Z= 0.815 Chirality : 0.053 0.392 484 Planarity : 0.007 0.100 589 Dihedral : 5.860 25.534 471 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.72 % Allowed : 7.43 % Favored : 91.85 % Rotamer: Outliers : 4.94 % Allowed : 20.06 % Favored : 75.00 % Cbeta Deviations : 0.52 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: -1.81 (0.43), residues: 417 helix: -4.19 (0.50), residues: 19 sheet: -1.20 (0.50), residues: 114 loop : -0.98 (0.40), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 99 TYR 0.018 0.002 TYR D 52 PHE 0.015 0.002 PHE D 65 TRP 0.019 0.002 TRP E 47 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 3322) covalent geometry : angle 1.40396 ( 4515) SS BOND : bond 0.00845 ( 5) SS BOND : angle 1.76093 ( 10) hydrogen bonds : bond 0.03095 ( 62) hydrogen bonds : angle 6.77268 ( 156) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 SER cc_start: 0.8211 (m) cc_final: 0.7792 (p) REVERT: A 376 THR cc_start: 0.8868 (t) cc_final: 0.8617 (p) REVERT: A 389 ASP cc_start: 0.7323 (t70) cc_final: 0.6800 (t0) REVERT: A 452 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8216 (mt) REVERT: E 11 LEU cc_start: 0.7954 (tp) cc_final: 0.7132 (mp) outliers start: 17 outliers final: 16 residues processed: 75 average time/residue: 0.0721 time to fit residues: 6.5683 Evaluate side-chains 80 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 45 GLN Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.0000 chunk 24 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 GLN ** 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 = 0.4302 r_free = 0.4302 target = 0.162824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.118761 restraints weight = 5403.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.121891 restraints weight = 3358.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.124147 restraints weight = 2468.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.125262 restraints weight = 2024.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.125870 restraints weight = 1815.604| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.6056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.580 3327 Z= 0.768 Angle : 1.264 48.919 4525 Z= 0.704 Chirality : 0.053 0.378 484 Planarity : 0.010 0.186 589 Dihedral : 5.861 25.534 471 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 20.89 Ramachandran Plot: Outliers : 0.72 % Allowed : 7.43 % Favored : 91.85 % Rotamer: Outliers : 4.94 % Allowed : 20.35 % Favored : 74.71 % Cbeta Deviations : 0.52 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % 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: -1.81 (0.43), residues: 417 helix: -4.19 (0.50), residues: 19 sheet: -1.20 (0.50), residues: 114 loop : -0.98 (0.40), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 99 TYR 0.018 0.002 TYR D 52 PHE 0.015 0.002 PHE D 65 TRP 0.019 0.002 TRP E 47 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.01657 ( 3322) covalent geometry : angle 1.26314 ( 4515) SS BOND : bond 0.00844 ( 5) SS BOND : angle 1.76114 ( 10) hydrogen bonds : bond 0.03094 ( 62) hydrogen bonds : angle 6.77277 ( 156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 784.59 seconds wall clock time: 14 minutes 5.25 seconds (845.25 seconds total)