Starting phenix.real_space_refine on Thu Jul 24 15:06:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cff_45544/07_2025/9cff_45544.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cff_45544/07_2025/9cff_45544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cff_45544/07_2025/9cff_45544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cff_45544/07_2025/9cff_45544.map" model { file = "/net/cci-nas-00/data/ceres_data/9cff_45544/07_2025/9cff_45544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cff_45544/07_2025/9cff_45544.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 14 5.16 5 C 2077 2.51 5 N 554 2.21 5 O 619 1.98 5 H 3134 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6398 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1748 Classifications: {'peptide': 115} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "L" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1653 Classifications: {'peptide': 108} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "A" Number of atoms: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2997 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 14, 'TRANS': 179} Time building chain proxies: 5.04, per 1000 atoms: 0.79 Number of scatterers: 6398 At special positions: 0 Unit cell: (64.74, 91.3, 88.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 619 8.00 N 554 7.00 C 2077 6.00 H 3134 1.00 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 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 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: 1.56 Conformation dependent library (CDL) restraints added in 573.4 milliseconds 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 11 sheets defined 13.2% alpha, 40.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.566A pdb=" N ASN H 32 " --> pdb=" O ILE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.322A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.252A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.756A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) 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 'H' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.970A pdb=" N TYR H 33 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.530A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ARG L 91 " --> pdb=" O THR L 98 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N THR L 98 " --> pdb=" O ARG L 91 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASP L 93 " --> pdb=" O ARG L 96 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.530A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR L 86 " --> pdb=" O THR L 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.107A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.107A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.863A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 129 hydrogen bonds defined for protein. 300 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: 2.61 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3134 1.03 - 1.23: 73 1.23 - 1.43: 1406 1.43 - 1.62: 1856 1.62 - 1.82: 16 Bond restraints: 6485 Sorted by residual: bond pdb=" N GLU H 1 " pdb=" H3 GLU H 1 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" N GLU L 1 " pdb=" H3 GLU L 1 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" N GLU L 1 " pdb=" H2 GLU L 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" N GLU H 1 " pdb=" H2 GLU H 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" CG PRO A 479 " pdb=" CD PRO A 479 " ideal model delta sigma weight residual 1.503 1.413 0.090 3.40e-02 8.65e+02 6.94e+00 ... (remaining 6480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.61: 11641 4.61 - 9.21: 5 9.21 - 13.82: 2 13.82 - 18.43: 1 18.43 - 23.03: 1 Bond angle restraints: 11650 Sorted by residual: angle pdb=" H1 GLU L 1 " pdb=" N GLU L 1 " pdb=" H2 GLU L 1 " ideal model delta sigma weight residual 109.47 86.44 23.03 3.00e+00 1.11e-01 5.89e+01 angle pdb=" N PRO A 479 " pdb=" CD PRO A 479 " pdb=" CG PRO A 479 " ideal model delta sigma weight residual 103.20 92.94 10.26 1.50e+00 4.44e-01 4.68e+01 angle pdb=" CA PRO A 479 " pdb=" N PRO A 479 " pdb=" CD PRO A 479 " ideal model delta sigma weight residual 112.00 104.68 7.32 1.40e+00 5.10e-01 2.74e+01 angle pdb=" H1 GLU L 1 " pdb=" N GLU L 1 " pdb=" H3 GLU L 1 " ideal model delta sigma weight residual 109.47 124.83 -15.36 3.00e+00 1.11e-01 2.62e+01 angle pdb=" CA PRO A 479 " pdb=" CB PRO A 479 " pdb=" CG PRO A 479 " ideal model delta sigma weight residual 104.50 95.47 9.03 1.90e+00 2.77e-01 2.26e+01 ... (remaining 11645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 2780 17.88 - 35.76: 231 35.76 - 53.64: 79 53.64 - 71.51: 28 71.51 - 89.39: 7 Dihedral angle restraints: 3125 sinusoidal: 1665 harmonic: 1460 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -159.50 73.50 1 1.00e+01 1.00e-02 6.87e+01 dihedral pdb=" CA CYS A 480 " pdb=" C CYS A 480 " pdb=" N ASN A 481 " pdb=" CA ASN A 481 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA CYS A 336 " pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " ideal model delta sinusoidal sigma weight residual 79.00 12.21 66.79 1 2.00e+01 2.50e-03 1.45e+01 ... (remaining 3122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 233 0.027 - 0.053: 178 0.053 - 0.080: 30 0.080 - 0.106: 20 0.106 - 0.133: 25 Chirality restraints: 486 Sorted by residual: chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE H 92 " pdb=" N ILE H 92 " pdb=" C ILE H 92 " pdb=" CB ILE H 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA VAL A 524 " pdb=" N VAL A 524 " pdb=" C VAL A 524 " pdb=" CB VAL A 524 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 483 not shown) Planarity restraints: 984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 383 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO A 384 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " -0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO A 521 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 478 " -0.027 5.00e-02 4.00e+02 3.90e-02 2.44e+00 pdb=" N PRO A 479 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 479 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 479 " -0.022 5.00e-02 4.00e+02 ... (remaining 981 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 607 2.22 - 2.82: 13455 2.82 - 3.41: 16672 3.41 - 4.01: 24164 4.01 - 4.60: 36247 Nonbonded interactions: 91145 Sorted by model distance: nonbonded pdb="HH22 ARG A 454 " pdb=" O SER A 469 " model vdw 1.625 2.450 nonbonded pdb="HH11 ARG H 97 " pdb=" OD2 ASP H 104 " model vdw 1.629 2.450 nonbonded pdb="HH22 ARG H 97 " pdb=" OD1 ASN A 487 " model vdw 1.630 2.450 nonbonded pdb=" HG SER A 438 " pdb=" OD2 ASP A 442 " model vdw 1.644 2.450 nonbonded pdb=" O TRP A 353 " pdb="HH21 ARG A 466 " model vdw 1.657 2.450 ... (remaining 91140 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 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: 0.110 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.390 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:14.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 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 : 0.004 0.090 3357 Z= 0.157 Angle : 0.626 11.425 4570 Z= 0.327 Chirality : 0.045 0.133 486 Planarity : 0.005 0.050 595 Dihedral : 15.883 89.393 1204 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.38 % Favored : 95.38 % Rotamer: Outliers : 1.69 % Allowed : 16.06 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.42), residues: 411 helix: -3.43 (0.74), residues: 33 sheet: 0.33 (0.48), residues: 127 loop : -0.19 (0.40), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 353 HIS 0.003 0.001 HIS L 31 PHE 0.008 0.001 PHE A 429 TYR 0.011 0.001 TYR H 33 ARG 0.001 0.000 ARG A 509 Details of bonding type rmsd hydrogen bonds : bond 0.22414 ( 113) hydrogen bonds : angle 10.75876 ( 300) SS BOND : bond 0.00250 ( 6) SS BOND : angle 1.04858 ( 12) covalent geometry : bond 0.00387 ( 3351) covalent geometry : angle 0.62475 ( 4558) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 443 is missing expected H atoms. Skipping. Evaluate side-chains 54 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 53 average time/residue: 2.7772 time to fit residues: 151.0077 Evaluate side-chains 31 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain A residue 339 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.053401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.044042 restraints weight = 29548.674| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 3.14 r_work: 0.2592 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3357 Z= 0.149 Angle : 0.588 7.159 4570 Z= 0.301 Chirality : 0.044 0.130 486 Planarity : 0.005 0.050 595 Dihedral : 5.909 57.848 469 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.89 % Favored : 95.86 % Rotamer: Outliers : 2.82 % Allowed : 18.87 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.42), residues: 411 helix: -3.38 (0.72), residues: 33 sheet: 0.54 (0.48), residues: 124 loop : -0.13 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 105 HIS 0.002 0.001 HIS L 31 PHE 0.005 0.001 PHE A 497 TYR 0.008 0.001 TYR H 33 ARG 0.004 0.001 ARG L 18 Details of bonding type rmsd hydrogen bonds : bond 0.03999 ( 113) hydrogen bonds : angle 6.98283 ( 300) SS BOND : bond 0.00291 ( 6) SS BOND : angle 0.92768 ( 12) covalent geometry : bond 0.00344 ( 3351) covalent geometry : angle 0.58670 ( 4558) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 443 is missing expected H atoms. Skipping. Evaluate side-chains 41 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 106 GLU cc_start: 0.4104 (tt0) cc_final: 0.3863 (tt0) REVERT: A 390 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8078 (mp) REVERT: A 466 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7258 (ttm110) REVERT: A 516 GLU cc_start: 0.8123 (tt0) cc_final: 0.7885 (tt0) outliers start: 10 outliers final: 4 residues processed: 41 average time/residue: 2.4642 time to fit residues: 104.2361 Evaluate side-chains 36 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 466 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN A 519 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.052631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.043365 restraints weight = 29879.806| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 3.12 r_work: 0.2575 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3357 Z= 0.153 Angle : 0.552 5.093 4570 Z= 0.281 Chirality : 0.044 0.126 486 Planarity : 0.004 0.037 595 Dihedral : 5.429 56.384 465 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.89 % Favored : 95.86 % Rotamer: Outliers : 2.54 % Allowed : 19.15 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.42), residues: 411 helix: -3.16 (0.74), residues: 33 sheet: 0.68 (0.47), residues: 124 loop : -0.16 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.003 0.001 HIS A 519 PHE 0.005 0.001 PHE A 429 TYR 0.008 0.001 TYR H 33 ARG 0.003 0.000 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.03143 ( 113) hydrogen bonds : angle 6.19200 ( 300) SS BOND : bond 0.00296 ( 6) SS BOND : angle 0.83690 ( 12) covalent geometry : bond 0.00359 ( 3351) covalent geometry : angle 0.55071 ( 4558) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 443 is missing expected H atoms. Skipping. Evaluate side-chains 39 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 106 GLU cc_start: 0.3987 (tt0) cc_final: 0.3712 (tp30) REVERT: A 390 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8155 (mp) REVERT: A 516 GLU cc_start: 0.8289 (tt0) cc_final: 0.7994 (tt0) REVERT: A 519 HIS cc_start: 0.8130 (m90) cc_final: 0.7813 (t70) outliers start: 9 outliers final: 5 residues processed: 38 average time/residue: 2.4946 time to fit residues: 97.7648 Evaluate side-chains 35 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** 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 = 0.2945 r_free = 0.2945 target = 0.051721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.042718 restraints weight = 31079.769| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 3.12 r_work: 0.2615 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 3357 Z= 0.212 Angle : 0.565 4.582 4570 Z= 0.288 Chirality : 0.044 0.124 486 Planarity : 0.004 0.034 595 Dihedral : 5.450 53.083 465 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.87 % Favored : 94.89 % Rotamer: Outliers : 2.25 % Allowed : 18.59 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.42), residues: 411 helix: -2.79 (0.90), residues: 27 sheet: 0.53 (0.45), residues: 129 loop : -0.21 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.002 0.001 HIS L 31 PHE 0.006 0.001 PHE A 429 TYR 0.011 0.001 TYR H 33 ARG 0.002 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.03019 ( 113) hydrogen bonds : angle 5.87774 ( 300) SS BOND : bond 0.00360 ( 6) SS BOND : angle 0.95179 ( 12) covalent geometry : bond 0.00493 ( 3351) covalent geometry : angle 0.56367 ( 4558) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 443 is missing expected H atoms. Skipping. Evaluate side-chains 40 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 102 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8357 (mt-10) REVERT: L 106 GLU cc_start: 0.4073 (tt0) cc_final: 0.3698 (tp30) REVERT: A 390 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8187 (mp) REVERT: A 519 HIS cc_start: 0.8226 (m90) cc_final: 0.7823 (t-170) outliers start: 8 outliers final: 5 residues processed: 39 average time/residue: 2.8195 time to fit residues: 114.0030 Evaluate side-chains 37 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 36 optimal weight: 0.0670 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 0.0980 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.052569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.043683 restraints weight = 30649.231| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 3.10 r_work: 0.2637 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3357 Z= 0.119 Angle : 0.530 4.868 4570 Z= 0.270 Chirality : 0.044 0.128 486 Planarity : 0.004 0.029 595 Dihedral : 5.137 52.035 465 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.65 % Favored : 96.11 % Rotamer: Outliers : 1.97 % Allowed : 19.72 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.42), residues: 411 helix: -2.51 (0.96), residues: 27 sheet: 0.64 (0.45), residues: 129 loop : -0.12 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.002 0.001 HIS L 31 PHE 0.003 0.001 PHE A 429 TYR 0.018 0.001 TYR A 369 ARG 0.003 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.02572 ( 113) hydrogen bonds : angle 5.56771 ( 300) SS BOND : bond 0.00273 ( 6) SS BOND : angle 0.63484 ( 12) covalent geometry : bond 0.00285 ( 3351) covalent geometry : angle 0.53006 ( 4558) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 443 is missing expected H atoms. Skipping. Evaluate side-chains 40 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 SER cc_start: 0.8772 (OUTLIER) cc_final: 0.8431 (m) REVERT: H 26 GLU cc_start: 0.7841 (pm20) cc_final: 0.7404 (pm20) REVERT: H 102 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8390 (mt-10) REVERT: L 106 GLU cc_start: 0.3930 (tt0) cc_final: 0.3434 (tp30) REVERT: A 519 HIS cc_start: 0.8135 (m90) cc_final: 0.7760 (t70) outliers start: 7 outliers final: 4 residues processed: 39 average time/residue: 2.2350 time to fit residues: 90.1614 Evaluate side-chains 36 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 0.0870 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.052650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.043726 restraints weight = 30149.738| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 3.07 r_work: 0.2638 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3357 Z= 0.125 Angle : 0.527 4.860 4570 Z= 0.268 Chirality : 0.043 0.126 486 Planarity : 0.004 0.029 595 Dihedral : 4.992 50.856 465 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.89 % Favored : 95.86 % Rotamer: Outliers : 1.69 % Allowed : 19.72 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.42), residues: 411 helix: -2.28 (1.01), residues: 27 sheet: 0.68 (0.45), residues: 129 loop : -0.15 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.002 0.001 HIS L 31 PHE 0.004 0.001 PHE A 392 TYR 0.007 0.001 TYR H 33 ARG 0.003 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.02544 ( 113) hydrogen bonds : angle 5.43852 ( 300) SS BOND : bond 0.00281 ( 6) SS BOND : angle 0.63985 ( 12) covalent geometry : bond 0.00301 ( 3351) covalent geometry : angle 0.52681 ( 4558) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 443 is missing expected H atoms. Skipping. Evaluate side-chains 36 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 SER cc_start: 0.8765 (OUTLIER) cc_final: 0.8434 (m) REVERT: H 26 GLU cc_start: 0.7873 (pm20) cc_final: 0.7520 (pm20) REVERT: H 102 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8352 (mt-10) REVERT: L 106 GLU cc_start: 0.3938 (tt0) cc_final: 0.3414 (tp30) REVERT: A 519 HIS cc_start: 0.8133 (m90) cc_final: 0.7733 (t70) outliers start: 6 outliers final: 4 residues processed: 36 average time/residue: 2.3224 time to fit residues: 86.4823 Evaluate side-chains 33 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.0040 chunk 1 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.052403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.043406 restraints weight = 30364.890| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 3.07 r_work: 0.2649 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3357 Z= 0.136 Angle : 0.534 5.248 4570 Z= 0.271 Chirality : 0.043 0.125 486 Planarity : 0.004 0.028 595 Dihedral : 4.934 50.048 465 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.41 % Favored : 96.35 % Rotamer: Outliers : 1.97 % Allowed : 20.00 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.43), residues: 411 helix: -2.19 (1.02), residues: 27 sheet: 0.71 (0.45), residues: 129 loop : -0.16 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 436 HIS 0.002 0.001 HIS L 31 PHE 0.004 0.001 PHE A 429 TYR 0.017 0.001 TYR A 369 ARG 0.003 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.02542 ( 113) hydrogen bonds : angle 5.38505 ( 300) SS BOND : bond 0.00280 ( 6) SS BOND : angle 0.68658 ( 12) covalent geometry : bond 0.00327 ( 3351) covalent geometry : angle 0.53363 ( 4558) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 443 is missing expected H atoms. Skipping. Evaluate side-chains 37 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 SER cc_start: 0.8766 (OUTLIER) cc_final: 0.8441 (m) REVERT: H 13 GLN cc_start: 0.9044 (mm-40) cc_final: 0.8592 (mp10) REVERT: H 26 GLU cc_start: 0.7878 (pm20) cc_final: 0.7530 (pm20) REVERT: H 102 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8371 (mt-10) REVERT: L 106 GLU cc_start: 0.3857 (tt0) cc_final: 0.3338 (tp30) REVERT: A 519 HIS cc_start: 0.8133 (m90) cc_final: 0.7716 (t-170) outliers start: 7 outliers final: 4 residues processed: 37 average time/residue: 2.2415 time to fit residues: 85.8814 Evaluate side-chains 34 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 21 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.052857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.043903 restraints weight = 30371.696| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 3.06 r_work: 0.2664 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3357 Z= 0.111 Angle : 0.526 5.579 4570 Z= 0.267 Chirality : 0.043 0.127 486 Planarity : 0.004 0.028 595 Dihedral : 4.766 48.943 465 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.89 % Favored : 95.86 % Rotamer: Outliers : 1.69 % Allowed : 20.28 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.42), residues: 411 helix: -2.33 (0.89), residues: 33 sheet: 0.86 (0.46), residues: 125 loop : -0.15 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.002 0.001 HIS L 31 PHE 0.004 0.001 PHE A 497 TYR 0.008 0.001 TYR A 369 ARG 0.004 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.02405 ( 113) hydrogen bonds : angle 5.25756 ( 300) SS BOND : bond 0.00272 ( 6) SS BOND : angle 0.60082 ( 12) covalent geometry : bond 0.00273 ( 3351) covalent geometry : angle 0.52613 ( 4558) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 443 is missing expected H atoms. Skipping. Evaluate side-chains 39 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 SER cc_start: 0.8739 (OUTLIER) cc_final: 0.8431 (m) REVERT: H 13 GLN cc_start: 0.9080 (mm-40) cc_final: 0.8670 (mp10) REVERT: H 26 GLU cc_start: 0.7865 (pm20) cc_final: 0.7506 (pm20) REVERT: H 102 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8389 (mt-10) REVERT: L 106 GLU cc_start: 0.3930 (tt0) cc_final: 0.3331 (tp30) REVERT: A 519 HIS cc_start: 0.8137 (m90) cc_final: 0.7677 (t70) outliers start: 6 outliers final: 2 residues processed: 39 average time/residue: 2.2869 time to fit residues: 92.2860 Evaluate side-chains 33 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.052937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.044038 restraints weight = 30917.650| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 3.09 r_work: 0.2662 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3357 Z= 0.106 Angle : 0.536 6.309 4570 Z= 0.272 Chirality : 0.043 0.125 486 Planarity : 0.004 0.029 595 Dihedral : 3.998 23.330 463 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.89 % Favored : 95.86 % Rotamer: Outliers : 1.13 % Allowed : 21.41 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.42), residues: 411 helix: -2.41 (0.85), residues: 35 sheet: 0.85 (0.46), residues: 125 loop : -0.21 (0.41), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 105 HIS 0.002 0.001 HIS L 31 PHE 0.004 0.001 PHE A 497 TYR 0.017 0.001 TYR A 369 ARG 0.004 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.02370 ( 113) hydrogen bonds : angle 5.16213 ( 300) SS BOND : bond 0.00265 ( 6) SS BOND : angle 0.57076 ( 12) covalent geometry : bond 0.00264 ( 3351) covalent geometry : angle 0.53583 ( 4558) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 443 is missing expected H atoms. Skipping. Evaluate side-chains 37 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 SER cc_start: 0.8708 (OUTLIER) cc_final: 0.8421 (m) REVERT: H 13 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8659 (mp10) REVERT: H 26 GLU cc_start: 0.7852 (pm20) cc_final: 0.7490 (pm20) REVERT: H 102 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8381 (mt-10) REVERT: L 106 GLU cc_start: 0.3955 (tt0) cc_final: 0.3352 (tp30) REVERT: A 519 HIS cc_start: 0.8111 (m90) cc_final: 0.7637 (t70) outliers start: 4 outliers final: 3 residues processed: 37 average time/residue: 2.3393 time to fit residues: 89.4151 Evaluate side-chains 34 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 0.0870 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.052882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.044025 restraints weight = 30773.721| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 3.08 r_work: 0.2681 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3357 Z= 0.120 Angle : 0.549 5.942 4570 Z= 0.276 Chirality : 0.043 0.133 486 Planarity : 0.004 0.063 595 Dihedral : 4.036 23.403 463 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.14 % Favored : 95.62 % Rotamer: Outliers : 1.13 % Allowed : 21.69 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.43), residues: 411 helix: -2.28 (0.96), residues: 29 sheet: 0.80 (0.46), residues: 126 loop : -0.23 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 436 HIS 0.003 0.001 HIS A 339 PHE 0.003 0.001 PHE A 342 TYR 0.007 0.001 TYR A 369 ARG 0.009 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.02427 ( 113) hydrogen bonds : angle 5.16095 ( 300) SS BOND : bond 0.00275 ( 6) SS BOND : angle 0.61026 ( 12) covalent geometry : bond 0.00296 ( 3351) covalent geometry : angle 0.54883 ( 4558) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 443 is missing expected H atoms. Skipping. Evaluate side-chains 33 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 SER cc_start: 0.8705 (OUTLIER) cc_final: 0.8425 (m) REVERT: H 13 GLN cc_start: 0.9071 (mm-40) cc_final: 0.8678 (mp10) REVERT: H 26 GLU cc_start: 0.7880 (pm20) cc_final: 0.7520 (pm20) REVERT: H 102 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8330 (mt-10) REVERT: L 106 GLU cc_start: 0.4011 (tt0) cc_final: 0.3391 (tp30) REVERT: A 519 HIS cc_start: 0.8156 (m90) cc_final: 0.7660 (t70) outliers start: 4 outliers final: 2 residues processed: 33 average time/residue: 3.6224 time to fit residues: 124.0271 Evaluate side-chains 32 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.053461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.044016 restraints weight = 29833.471| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 3.18 r_work: 0.2608 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3357 Z= 0.117 Angle : 0.548 6.504 4570 Z= 0.277 Chirality : 0.043 0.124 486 Planarity : 0.004 0.059 595 Dihedral : 3.998 23.546 463 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.65 % Favored : 96.11 % Rotamer: Outliers : 0.85 % Allowed : 22.25 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.42), residues: 411 helix: -2.42 (0.84), residues: 35 sheet: 0.88 (0.46), residues: 125 loop : -0.21 (0.41), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 436 HIS 0.003 0.001 HIS A 339 PHE 0.003 0.001 PHE A 497 TYR 0.015 0.001 TYR A 369 ARG 0.010 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.02383 ( 113) hydrogen bonds : angle 5.14877 ( 300) SS BOND : bond 0.00269 ( 6) SS BOND : angle 0.59801 ( 12) covalent geometry : bond 0.00290 ( 3351) covalent geometry : angle 0.54773 ( 4558) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5855.43 seconds wall clock time: 103 minutes 47.92 seconds (6227.92 seconds total)