Starting phenix.real_space_refine on Wed Jul 1 22:16:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d8r_27255/07_2026/8d8r_27255.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d8r_27255/07_2026/8d8r_27255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d8r_27255/07_2026/8d8r_27255.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d8r_27255/07_2026/8d8r_27255.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d8r_27255/07_2026/8d8r_27255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d8r_27255/07_2026/8d8r_27255.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8d8r_27255/07_2026/8d8r_27255.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d8r_27255/07_2026/8d8r_27255.cif" } resolution = 4.1 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= -0.002 sd= 0.039 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 2102 2.51 5 N 562 2.21 5 O 640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3323 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 832 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.95, per 1000 atoms: 0.29 Number of scatterers: 3323 At special positions: 0 Unit cell: (69.564, 59.024, 102.238, 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 640 8.00 N 562 7.00 C 2102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 97 " - pdb=" SG CYS H 102 " distance=2.19 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.08 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.21 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " Time building additional restraints: 0.25 Conformation dependent library (CDL) restraints added in 119.9 milliseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 776 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 9 sheets defined 15.1% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.590A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 60 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.799A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.510A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.449A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.531A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.510A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.612A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 119 hydrogen bonds defined for protein. 267 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: 0.53 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: 1.20 - 1.33: 863 1.33 - 1.46: 844 1.46 - 1.58: 1674 1.58 - 1.71: 0 1.71 - 1.83: 24 Bond restraints: 3405 Sorted by residual: bond pdb=" CB PHE H 106 " pdb=" CG PHE H 106 " ideal model delta sigma weight residual 1.502 1.444 0.058 2.30e-02 1.89e+03 6.34e+00 bond pdb=" CG ASP L 82 " pdb=" OD2 ASP L 82 " ideal model delta sigma weight residual 1.249 1.204 0.045 1.90e-02 2.77e+03 5.51e+00 bond pdb=" CD GLU H 10 " pdb=" OE1 GLU H 10 " ideal model delta sigma weight residual 1.249 1.205 0.044 1.90e-02 2.77e+03 5.46e+00 bond pdb=" CB VAL A 350 " pdb=" CG1 VAL A 350 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.29e+00 bond pdb=" CG ASP A 389 " pdb=" OD2 ASP A 389 " ideal model delta sigma weight residual 1.249 1.205 0.044 1.90e-02 2.77e+03 5.29e+00 ... (remaining 3400 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 3935 1.62 - 3.24: 561 3.24 - 4.85: 95 4.85 - 6.47: 24 6.47 - 8.09: 7 Bond angle restraints: 4622 Sorted by residual: angle pdb=" C ALA H 94 " pdb=" N PRO H 95 " pdb=" CA PRO H 95 " ideal model delta sigma weight residual 119.78 127.87 -8.09 1.03e+00 9.43e-01 6.17e+01 angle pdb=" C GLY H 8 " pdb=" N PRO H 9 " pdb=" CA PRO H 9 " ideal model delta sigma weight residual 119.76 127.18 -7.42 1.03e+00 9.43e-01 5.19e+01 angle pdb=" C ILE L 58 " pdb=" N PRO L 59 " pdb=" CA PRO L 59 " ideal model delta sigma weight residual 119.78 126.71 -6.93 1.03e+00 9.43e-01 4.53e+01 angle pdb=" C SER A 383 " pdb=" N PRO A 384 " pdb=" CA PRO A 384 " ideal model delta sigma weight residual 119.56 126.31 -6.75 1.02e+00 9.61e-01 4.38e+01 angle pdb=" C GLN A 498 " pdb=" N PRO A 499 " pdb=" CA PRO A 499 " ideal model delta sigma weight residual 119.56 125.98 -6.42 1.02e+00 9.61e-01 3.96e+01 ... (remaining 4617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.51: 1912 16.51 - 33.03: 61 33.03 - 49.54: 15 49.54 - 66.05: 7 66.05 - 82.56: 6 Dihedral angle restraints: 2001 sinusoidal: 777 harmonic: 1224 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 145.99 -52.99 1 1.00e+01 1.00e-02 3.82e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 55.61 37.39 1 1.00e+01 1.00e-02 1.97e+01 dihedral pdb=" CA ALA H 94 " pdb=" C ALA H 94 " pdb=" N PRO H 95 " pdb=" CA PRO H 95 " ideal model delta harmonic sigma weight residual 180.00 158.74 21.26 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 1998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 274 0.041 - 0.081: 153 0.081 - 0.122: 51 0.122 - 0.163: 16 0.163 - 0.203: 4 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ASN H 103 " pdb=" N ASN H 103 " pdb=" C ASN H 103 " pdb=" CB ASN H 103 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.45e-01 chirality pdb=" CB ILE A 402 " pdb=" CA ILE A 402 " pdb=" CG1 ILE A 402 " pdb=" CG2 ILE A 402 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.24e-01 ... (remaining 495 not shown) Planarity restraints: 597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 423 " 0.045 2.00e-02 2.50e+03 2.45e-02 1.20e+01 pdb=" CG TYR A 423 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR A 423 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 423 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR A 423 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR A 423 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 423 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 423 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU L 78 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C LEU L 78 " 0.034 2.00e-02 2.50e+03 pdb=" O LEU L 78 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU L 79 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 488 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C CYS A 488 " -0.033 2.00e-02 2.50e+03 pdb=" O CYS A 488 " 0.012 2.00e-02 2.50e+03 pdb=" N TYR A 489 " 0.011 2.00e-02 2.50e+03 ... (remaining 594 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 1757 2.99 - 3.47: 2933 3.47 - 3.94: 5421 3.94 - 4.42: 6051 4.42 - 4.90: 9996 Nonbonded interactions: 26158 Sorted by model distance: nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.512 3.040 nonbonded pdb=" O LYS H 13 " pdb=" OG1 THR H 16 " model vdw 2.538 3.040 nonbonded pdb=" N TYR A 380 " pdb=" N GLY A 381 " model vdw 2.550 2.560 nonbonded pdb=" O SER H 31 " pdb=" OG SER H 101 " model vdw 2.554 3.040 nonbonded pdb=" OG SER H 98 " pdb=" N SER H 99 " model vdw 2.556 3.120 ... (remaining 26153 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: 4.460 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.280 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6137 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 : 0.012 0.183 3412 Z= 0.636 Angle : 1.263 8.091 4637 Z= 0.872 Chirality : 0.056 0.203 498 Planarity : 0.006 0.024 596 Dihedral : 10.996 82.563 1207 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.96 (0.43), residues: 419 helix: -4.23 (0.36), residues: 34 sheet: 1.42 (0.42), residues: 150 loop : 2.42 (0.44), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 466 TYR 0.045 0.005 TYR A 423 PHE 0.016 0.004 PHE A 400 TRP 0.017 0.005 TRP H 47 HIS 0.002 0.001 HIS L 90 Details of bonding type rmsd/Z covalent geometry : bond 0.01100 / 0.60 ( 3405) covalent geometry : angle 1.25470 / 0.87 ( 4622) SS BOND : bond 0.10135 / 4.23 ( 6) SS BOND : angle 3.11307 / 1.58 ( 12) hydrogen bonds : bond 0.18158 / 11.35 ( 112) hydrogen bonds : angle 9.30121 / 6.26 ( 267) link_NAG-ASN : bond 0.07200 / 3.79 ( 1) link_NAG-ASN : angle 1.35761 / 0.80 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 2 ILE cc_start: 0.7054 (mm) cc_final: 0.6774 (mm) REVERT: H 20 VAL cc_start: 0.8368 (t) cc_final: 0.7917 (p) REVERT: H 57 THR cc_start: 0.6787 (p) cc_final: 0.6535 (t) REVERT: A 354 ASN cc_start: 0.7161 (t0) cc_final: 0.6751 (p0) REVERT: A 427 ASP cc_start: 0.8005 (m-30) cc_final: 0.7565 (p0) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.0716 time to fit residues: 10.7302 Evaluate side-chains 76 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 0.0270 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.194124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.171201 restraints weight = 6421.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.175922 restraints weight = 4102.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.179173 restraints weight = 2888.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.181625 restraints weight = 2185.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.183257 restraints weight = 1725.262| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6238 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3412 Z= 0.176 Angle : 0.650 5.993 4637 Z= 0.357 Chirality : 0.045 0.132 498 Planarity : 0.005 0.063 596 Dihedral : 5.028 18.839 470 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.28 % Allowed : 1.94 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.07 (0.42), residues: 419 helix: -3.70 (0.63), residues: 28 sheet: 0.80 (0.40), residues: 158 loop : 1.48 (0.44), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 61 TYR 0.018 0.002 TYR A 453 PHE 0.036 0.002 PHE A 400 TRP 0.021 0.003 TRP H 36 HIS 0.001 0.001 HIS L 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 ( 3405) covalent geometry : angle 0.64903 / 0.36 ( 4622) SS BOND : bond 0.00272 / 0.13 ( 6) SS BOND : angle 0.50229 / 0.29 ( 12) hydrogen bonds : bond 0.04263 / 2.83 ( 112) hydrogen bonds : angle 6.92857 / 4.61 ( 267) link_NAG-ASN : bond 0.00080 / 0.04 ( 1) link_NAG-ASN : angle 1.65247 / 0.90 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.8475 (m100) cc_final: 0.7929 (m100) REVERT: A 370 ASN cc_start: 0.7006 (m-40) cc_final: 0.6789 (p0) REVERT: A 403 ARG cc_start: 0.7963 (mtp85) cc_final: 0.7377 (mtm110) REVERT: A 427 ASP cc_start: 0.7979 (m-30) cc_final: 0.7521 (p0) outliers start: 1 outliers final: 1 residues processed: 98 average time/residue: 0.0648 time to fit residues: 7.8221 Evaluate side-chains 85 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.0670 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 0.0020 chunk 35 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 overall best weight: 0.4326 ------------------------------------------------------------------------------- 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 = 0.4265 r_free = 0.4265 target = 0.192682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.170131 restraints weight = 6266.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.174760 restraints weight = 4025.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.177981 restraints weight = 2829.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.180235 restraints weight = 2128.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.181957 restraints weight = 1685.933| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3412 Z= 0.149 Angle : 0.576 4.811 4637 Z= 0.322 Chirality : 0.043 0.133 498 Planarity : 0.005 0.052 596 Dihedral : 4.664 17.839 470 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.41), residues: 419 helix: -3.56 (0.65), residues: 28 sheet: 0.50 (0.39), residues: 151 loop : 1.00 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 346 TYR 0.017 0.002 TYR A 473 PHE 0.032 0.002 PHE H 29 TRP 0.019 0.002 TRP A 353 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 3405) covalent geometry : angle 0.57289 / 0.32 ( 4622) SS BOND : bond 0.00283 / 0.14 ( 6) SS BOND : angle 1.20474 / 0.49 ( 12) hydrogen bonds : bond 0.03862 / 2.55 ( 112) hydrogen bonds : angle 6.78222 / 4.42 ( 267) link_NAG-ASN : bond 0.00181 / 0.10 ( 1) link_NAG-ASN : angle 1.41952 / 0.80 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.8279 (m100) cc_final: 0.7796 (m100) REVERT: H 58 ASN cc_start: 0.7915 (p0) cc_final: 0.7699 (p0) REVERT: H 70 THR cc_start: 0.7891 (t) cc_final: 0.7327 (p) REVERT: H 79 TYR cc_start: 0.6989 (m-80) cc_final: 0.6769 (m-10) REVERT: H 111 GLN cc_start: 0.7380 (pm20) cc_final: 0.7175 (pt0) REVERT: H 118 SER cc_start: 0.5612 (t) cc_final: 0.5264 (p) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.0548 time to fit residues: 6.3720 Evaluate side-chains 82 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 90 HIS H 35 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.186554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.163294 restraints weight = 6300.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.167678 restraints weight = 4014.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.170783 restraints weight = 2854.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.173039 restraints weight = 2185.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.174691 restraints weight = 1761.401| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.6475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3412 Z= 0.193 Angle : 0.677 10.134 4637 Z= 0.368 Chirality : 0.047 0.281 498 Planarity : 0.006 0.051 596 Dihedral : 5.269 19.331 470 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.41), residues: 419 helix: -3.41 (0.74), residues: 28 sheet: 0.47 (0.39), residues: 151 loop : 0.55 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 54 TYR 0.028 0.003 TYR L 32 PHE 0.031 0.003 PHE A 400 TRP 0.019 0.003 TRP L 96 HIS 0.001 0.001 HIS L 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 ( 3405) covalent geometry : angle 0.67115 / 0.37 ( 4622) SS BOND : bond 0.00900 / 0.45 ( 6) SS BOND : angle 1.54732 / 0.66 ( 12) hydrogen bonds : bond 0.03763 / 2.49 ( 112) hydrogen bonds : angle 7.13413 / 4.76 ( 267) link_NAG-ASN : bond 0.00577 / 0.30 ( 1) link_NAG-ASN : angle 2.02767 / 1.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.8498 (m100) cc_final: 0.8223 (m100) REVERT: H 70 THR cc_start: 0.7903 (t) cc_final: 0.7578 (p) REVERT: H 79 TYR cc_start: 0.7119 (m-80) cc_final: 0.6793 (m-10) REVERT: H 111 GLN cc_start: 0.7658 (pm20) cc_final: 0.7414 (pt0) REVERT: A 516 GLU cc_start: 0.5667 (tt0) cc_final: 0.5421 (tt0) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.0605 time to fit residues: 7.0044 Evaluate side-chains 81 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.3980 chunk 38 optimal weight: 0.1980 chunk 7 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.0470 chunk 31 optimal weight: 0.2980 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 36 optimal weight: 0.3980 overall best weight: 0.2478 ------------------------------------------------------------------------------- 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 = 0.4266 r_free = 0.4266 target = 0.192877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.171219 restraints weight = 6240.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.175671 restraints weight = 4037.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.178681 restraints weight = 2856.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.180968 restraints weight = 2155.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.182526 restraints weight = 1693.246| |-----------------------------------------------------------------------------| r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6436 moved from start: 0.6673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3412 Z= 0.120 Angle : 0.690 16.166 4637 Z= 0.364 Chirality : 0.047 0.343 498 Planarity : 0.004 0.046 596 Dihedral : 4.770 19.298 470 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.28 % Allowed : 0.55 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.41), residues: 419 helix: -3.20 (0.87), residues: 28 sheet: 0.57 (0.41), residues: 139 loop : 0.41 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 346 TYR 0.022 0.002 TYR A 380 PHE 0.026 0.002 PHE H 29 TRP 0.025 0.003 TRP L 96 HIS 0.006 0.002 HIS L 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 3405) covalent geometry : angle 0.65575 / 0.35 ( 4622) SS BOND : bond 0.00155 / 0.08 ( 6) SS BOND : angle 3.86259 / 1.50 ( 12) hydrogen bonds : bond 0.03562 / 2.35 ( 112) hydrogen bonds : angle 6.35678 / 4.19 ( 267) link_NAG-ASN : bond 0.00858 / 0.45 ( 1) link_NAG-ASN : angle 3.66366 / 2.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 91 TYR cc_start: 0.7337 (m-10) cc_final: 0.6566 (m-10) REVERT: H 36 TRP cc_start: 0.8214 (m100) cc_final: 0.7878 (m100) REVERT: H 39 GLN cc_start: 0.7382 (tm-30) cc_final: 0.7052 (tm-30) REVERT: H 70 THR cc_start: 0.7920 (t) cc_final: 0.7488 (p) REVERT: H 79 TYR cc_start: 0.7096 (m-80) cc_final: 0.6758 (m-10) REVERT: H 111 GLN cc_start: 0.7424 (pm20) cc_final: 0.7051 (pt0) REVERT: A 516 GLU cc_start: 0.5537 (tt0) cc_final: 0.5316 (tt0) outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.0584 time to fit residues: 6.8262 Evaluate side-chains 81 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 37 optimal weight: 0.0570 chunk 3 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 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 = 0.4204 r_free = 0.4204 target = 0.187520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.164628 restraints weight = 6412.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.169052 restraints weight = 4105.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.172174 restraints weight = 2918.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.174175 restraints weight = 2223.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.175858 restraints weight = 1816.106| |-----------------------------------------------------------------------------| r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.7386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3412 Z= 0.188 Angle : 0.763 16.083 4637 Z= 0.402 Chirality : 0.049 0.312 498 Planarity : 0.005 0.040 596 Dihedral : 5.427 26.079 470 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.41), residues: 419 helix: -3.53 (0.70), residues: 28 sheet: 0.58 (0.41), residues: 141 loop : 0.04 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 54 TYR 0.026 0.003 TYR A 380 PHE 0.040 0.003 PHE A 400 TRP 0.028 0.003 TRP L 96 HIS 0.004 0.002 HIS L 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 ( 3405) covalent geometry : angle 0.72642 / 0.39 ( 4622) SS BOND : bond 0.00819 / 0.41 ( 6) SS BOND : angle 4.45734 / 1.80 ( 12) hydrogen bonds : bond 0.03886 / 2.55 ( 112) hydrogen bonds : angle 6.77844 / 4.49 ( 267) link_NAG-ASN : bond 0.00706 / 0.37 ( 1) link_NAG-ASN : angle 2.58644 / 1.51 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: L 91 TYR cc_start: 0.7454 (m-10) cc_final: 0.6735 (m-10) REVERT: H 30 MET cc_start: 0.8875 (mmm) cc_final: 0.8637 (mmm) REVERT: H 36 TRP cc_start: 0.8492 (m100) cc_final: 0.8239 (m100) REVERT: H 39 GLN cc_start: 0.7440 (tm-30) cc_final: 0.7166 (tm-30) REVERT: H 70 THR cc_start: 0.7986 (t) cc_final: 0.7643 (p) REVERT: H 111 GLN cc_start: 0.7791 (pm20) cc_final: 0.7564 (pt0) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.0687 time to fit residues: 7.8381 Evaluate side-chains 82 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 36 optimal weight: 0.0670 chunk 27 optimal weight: 0.9980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.189772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.166879 restraints weight = 6543.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.171329 restraints weight = 4262.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.174461 restraints weight = 3051.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.176614 restraints weight = 2333.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.178280 restraints weight = 1881.675| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.7566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3412 Z= 0.148 Angle : 0.703 14.284 4637 Z= 0.371 Chirality : 0.048 0.282 498 Planarity : 0.004 0.040 596 Dihedral : 5.131 26.073 470 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.28 % Allowed : 1.39 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.42), residues: 419 helix: -3.61 (0.71), residues: 28 sheet: 0.85 (0.45), residues: 127 loop : -0.14 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 45 TYR 0.028 0.002 TYR A 453 PHE 0.017 0.002 PHE A 400 TRP 0.024 0.003 TRP H 50 HIS 0.002 0.001 HIS L 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 3405) covalent geometry : angle 0.67185 / 0.36 ( 4622) SS BOND : bond 0.00491 / 0.25 ( 6) SS BOND : angle 3.96463 / 1.59 ( 12) hydrogen bonds : bond 0.03567 / 2.33 ( 112) hydrogen bonds : angle 6.54938 / 4.33 ( 267) link_NAG-ASN : bond 0.00587 / 0.31 ( 1) link_NAG-ASN : angle 2.29013 / 1.35 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 30 MET cc_start: 0.8942 (mmm) cc_final: 0.8645 (mmm) REVERT: H 36 TRP cc_start: 0.8413 (m100) cc_final: 0.7929 (m100) REVERT: H 70 THR cc_start: 0.7986 (t) cc_final: 0.7711 (p) REVERT: H 80 MET cc_start: 0.4870 (mtp) cc_final: 0.4272 (mtp) REVERT: H 89 VAL cc_start: 0.7580 (t) cc_final: 0.7342 (t) REVERT: H 111 GLN cc_start: 0.7700 (pm20) cc_final: 0.7431 (pt0) REVERT: A 403 ARG cc_start: 0.8119 (mtp85) cc_final: 0.7901 (mtp-110) REVERT: A 428 ASP cc_start: 0.7367 (t0) cc_final: 0.7158 (t0) REVERT: A 516 GLU cc_start: 0.6216 (tt0) cc_final: 0.5565 (tt0) outliers start: 1 outliers final: 0 residues processed: 89 average time/residue: 0.0650 time to fit residues: 7.1130 Evaluate side-chains 79 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 0.2980 chunk 3 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 17 optimal weight: 0.3980 chunk 29 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 35 optimal weight: 0.0040 chunk 16 optimal weight: 0.0170 chunk 37 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 overall best weight: 0.2430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 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 = 0.4265 r_free = 0.4265 target = 0.192739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.170628 restraints weight = 6557.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.175007 restraints weight = 4207.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.178213 restraints weight = 2982.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.180291 restraints weight = 2257.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.182064 restraints weight = 1812.516| |-----------------------------------------------------------------------------| r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.7832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3412 Z= 0.119 Angle : 0.661 12.316 4637 Z= 0.346 Chirality : 0.048 0.283 498 Planarity : 0.004 0.040 596 Dihedral : 4.877 25.892 470 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.42), residues: 419 helix: -3.27 (0.71), residues: 34 sheet: 0.93 (0.45), residues: 129 loop : -0.23 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 45 TYR 0.021 0.002 TYR A 453 PHE 0.017 0.001 PHE H 29 TRP 0.030 0.002 TRP H 50 HIS 0.002 0.001 HIS L 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 3405) covalent geometry : angle 0.62825 / 0.33 ( 4622) SS BOND : bond 0.00363 / 0.18 ( 6) SS BOND : angle 3.93927 / 1.57 ( 12) hydrogen bonds : bond 0.03346 / 2.18 ( 112) hydrogen bonds : angle 6.41300 / 4.25 ( 267) link_NAG-ASN : bond 0.00502 / 0.26 ( 1) link_NAG-ASN : angle 2.21514 / 1.30 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.8174 (m100) cc_final: 0.7906 (m100) REVERT: H 70 THR cc_start: 0.7934 (t) cc_final: 0.7692 (p) REVERT: H 111 GLN cc_start: 0.7598 (pm20) cc_final: 0.7285 (pt0) REVERT: A 473 TYR cc_start: 0.8152 (t80) cc_final: 0.7812 (t80) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0693 time to fit residues: 7.5577 Evaluate side-chains 77 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 0.0570 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 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 = 0.4201 r_free = 0.4201 target = 0.186423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.164002 restraints weight = 6620.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.168027 restraints weight = 4362.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.170965 restraints weight = 3177.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.172915 restraints weight = 2473.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.174524 restraints weight = 2034.055| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.8149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3412 Z= 0.191 Angle : 0.736 13.499 4637 Z= 0.386 Chirality : 0.050 0.282 498 Planarity : 0.005 0.041 596 Dihedral : 5.421 31.626 470 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.41), residues: 419 helix: -3.53 (0.68), residues: 34 sheet: 0.58 (0.44), residues: 129 loop : -0.39 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 45 TYR 0.027 0.003 TYR A 423 PHE 0.023 0.002 PHE A 400 TRP 0.040 0.003 TRP H 50 HIS 0.002 0.001 HIS L 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 ( 3405) covalent geometry : angle 0.70188 / 0.37 ( 4622) SS BOND : bond 0.00278 / 0.15 ( 6) SS BOND : angle 4.26726 / 1.72 ( 12) hydrogen bonds : bond 0.03755 / 2.47 ( 112) hydrogen bonds : angle 6.82088 / 4.56 ( 267) link_NAG-ASN : bond 0.00334 / 0.18 ( 1) link_NAG-ASN : angle 2.25188 / 1.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: H 36 TRP cc_start: 0.8533 (m100) cc_final: 0.8052 (m100) REVERT: H 89 VAL cc_start: 0.7563 (t) cc_final: 0.7362 (t) REVERT: A 375 SER cc_start: 0.8861 (p) cc_final: 0.8624 (t) REVERT: A 473 TYR cc_start: 0.8231 (t80) cc_final: 0.7883 (t80) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.0749 time to fit residues: 8.0946 Evaluate side-chains 78 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 15 optimal weight: 0.0070 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 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 = 0.4225 r_free = 0.4225 target = 0.188634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.166187 restraints weight = 6400.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.170316 restraints weight = 4206.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.173298 restraints weight = 3061.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.175326 restraints weight = 2378.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.176841 restraints weight = 1942.759| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.8456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3412 Z= 0.165 Angle : 0.711 12.036 4637 Z= 0.373 Chirality : 0.050 0.272 498 Planarity : 0.004 0.041 596 Dihedral : 5.291 29.944 470 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.41), residues: 419 helix: -3.47 (0.72), residues: 34 sheet: 0.58 (0.44), residues: 129 loop : -0.47 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 509 TYR 0.025 0.002 TYR A 453 PHE 0.018 0.002 PHE A 400 TRP 0.037 0.003 TRP H 50 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 3405) covalent geometry : angle 0.67976 / 0.36 ( 4622) SS BOND : bond 0.00380 / 0.19 ( 6) SS BOND : angle 4.04386 / 1.62 ( 12) hydrogen bonds : bond 0.03711 / 2.43 ( 112) hydrogen bonds : angle 6.73845 / 4.54 ( 267) link_NAG-ASN : bond 0.00412 / 0.22 ( 1) link_NAG-ASN : angle 1.93215 / 1.07 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.8426 (m100) cc_final: 0.8221 (m100) REVERT: H 52 ILE cc_start: 0.7799 (mm) cc_final: 0.7501 (mm) REVERT: A 345 THR cc_start: 0.8466 (p) cc_final: 0.8240 (m) REVERT: A 375 SER cc_start: 0.8633 (p) cc_final: 0.8397 (t) REVERT: A 473 TYR cc_start: 0.8210 (t80) cc_final: 0.7909 (t80) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.0729 time to fit residues: 7.7578 Evaluate side-chains 80 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.0980 chunk 17 optimal weight: 0.7980 chunk 40 optimal weight: 0.0010 chunk 11 optimal weight: 0.0770 chunk 16 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.1980 overall best weight: 0.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 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 = 0.4293 r_free = 0.4293 target = 0.195400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.173338 restraints weight = 6270.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.177436 restraints weight = 4131.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.180444 restraints weight = 2961.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.182415 restraints weight = 2261.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.184119 restraints weight = 1828.854| |-----------------------------------------------------------------------------| r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.8586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 3412 Z= 0.113 Angle : 0.658 10.163 4637 Z= 0.340 Chirality : 0.049 0.284 498 Planarity : 0.004 0.044 596 Dihedral : 4.812 28.951 470 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.41), residues: 419 helix: -3.50 (0.68), residues: 35 sheet: 0.86 (0.45), residues: 129 loop : -0.43 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 509 TYR 0.021 0.002 TYR H 59 PHE 0.014 0.002 PHE H 29 TRP 0.020 0.002 TRP H 50 HIS 0.001 0.000 HIS L 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 3405) covalent geometry : angle 0.63102 / 0.33 ( 4622) SS BOND : bond 0.00279 / 0.14 ( 6) SS BOND : angle 3.62255 / 1.46 ( 12) hydrogen bonds : bond 0.03453 / 2.23 ( 112) hydrogen bonds : angle 6.25670 / 4.23 ( 267) link_NAG-ASN : bond 0.00354 / 0.19 ( 1) link_NAG-ASN : angle 2.05062 / 1.19 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 900.82 seconds wall clock time: 16 minutes 11.50 seconds (971.50 seconds total)