Starting phenix.real_space_refine on Mon Nov 17 16:15:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cfh_45546/11_2025/9cfh_45546.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cfh_45546/11_2025/9cfh_45546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cfh_45546/11_2025/9cfh_45546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cfh_45546/11_2025/9cfh_45546.map" model { file = "/net/cci-nas-00/data/ceres_data/9cfh_45546/11_2025/9cfh_45546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cfh_45546/11_2025/9cfh_45546.cif" } resolution = 3.1 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= -0.001 sd= 0.023 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 2078 2.51 5 N 551 2.21 5 O 619 1.98 5 H 3130 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6392 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3006 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 14, 'TRANS': 179} Chain: "H" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1733 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} Time building chain proxies: 1.46, per 1000 atoms: 0.23 Number of scatterers: 6392 At special positions: 0 Unit cell: (67.23, 87.98, 87.15, 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 551 7.00 C 2078 6.00 H 3130 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 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=2.05 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=2.04 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=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 284.0 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 9 sheets defined 13.7% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.827A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.506A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.682A pdb=" N THR H 90 " --> pdb=" O VAL H 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.589A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.078A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.724A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.757A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.082A pdb=" N TYR H 33 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.692A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 123 hydrogen bonds defined for protein. 291 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: 1.24 Time building geometry restraints manager: 0.80 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: 3130 1.03 - 1.23: 47 1.23 - 1.43: 1428 1.43 - 1.62: 1858 1.62 - 1.82: 16 Bond restraints: 6479 Sorted by residual: bond pdb=" N GLU H 1 " pdb=" H2 GLU H 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 1.23e+01 bond pdb=" N GLU L 1 " pdb=" H3 GLU L 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" N GLU H 1 " pdb=" H3 GLU H 1 " ideal model delta sigma weight residual 0.890 0.958 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C LEU A 335 " pdb=" N CYS A 336 " ideal model delta sigma weight residual 1.329 1.405 -0.076 3.03e-02 1.09e+03 6.32e+00 ... (remaining 6474 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.68: 11631 6.68 - 13.35: 7 13.35 - 20.03: 1 20.03 - 26.71: 1 26.71 - 33.38: 1 Bond angle restraints: 11641 Sorted by residual: angle pdb=" H1 GLU H 1 " pdb=" N GLU H 1 " pdb=" H3 GLU H 1 " ideal model delta sigma weight residual 109.47 76.09 33.38 3.00e+00 1.11e-01 1.24e+02 angle pdb=" H1 GLU H 1 " pdb=" N GLU H 1 " pdb=" H2 GLU H 1 " ideal model delta sigma weight residual 109.47 131.87 -22.40 3.00e+00 1.11e-01 5.57e+01 angle pdb=" CA PRO A 486 " pdb=" N PRO A 486 " pdb=" CD PRO A 486 " ideal model delta sigma weight residual 112.00 104.73 7.27 1.40e+00 5.10e-01 2.70e+01 angle pdb=" N CYS A 432 " pdb=" CA CYS A 432 " pdb=" C CYS A 432 " ideal model delta sigma weight residual 108.60 115.72 -7.12 1.46e+00 4.69e-01 2.38e+01 angle pdb=" H1 GLU L 1 " pdb=" N GLU L 1 " pdb=" H2 GLU L 1 " ideal model delta sigma weight residual 109.47 95.53 13.94 3.00e+00 1.11e-01 2.16e+01 ... (remaining 11636 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 2726 17.24 - 34.49: 275 34.49 - 51.73: 91 51.73 - 68.97: 24 68.97 - 86.22: 10 Dihedral angle restraints: 3126 sinusoidal: 1661 harmonic: 1465 Sorted by residual: dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 35.06 57.94 1 1.00e+01 1.00e-02 4.50e+01 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 93.00 137.82 -44.82 1 1.00e+01 1.00e-02 2.79e+01 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 -130.80 44.80 1 1.00e+01 1.00e-02 2.79e+01 ... (remaining 3123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 310 0.038 - 0.076: 127 0.076 - 0.115: 32 0.115 - 0.153: 17 0.153 - 0.191: 2 Chirality restraints: 488 Sorted by residual: chirality pdb=" CA CYS A 432 " pdb=" N CYS A 432 " pdb=" C CYS A 432 " pdb=" CB CYS A 432 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.11e-01 chirality pdb=" CA CYS A 379 " pdb=" N CYS A 379 " pdb=" C CYS A 379 " pdb=" CB CYS A 379 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.12e-01 chirality pdb=" CA VAL L 58 " pdb=" N VAL L 58 " pdb=" C VAL L 58 " pdb=" CB VAL L 58 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 ... (remaining 485 not shown) Planarity restraints: 983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 485 " -0.053 5.00e-02 4.00e+02 7.70e-02 9.49e+00 pdb=" N PRO A 486 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 486 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 486 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR H 52 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.12e+00 pdb=" N PRO H 53 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO H 53 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 53 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 43 " 0.018 5.00e-02 4.00e+02 2.69e-02 1.15e+00 pdb=" N PRO L 44 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO L 44 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO L 44 " 0.015 5.00e-02 4.00e+02 ... (remaining 980 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 1228 2.28 - 2.86: 13986 2.86 - 3.44: 16351 3.44 - 4.02: 23606 4.02 - 4.60: 34513 Nonbonded interactions: 89684 Sorted by model distance: nonbonded pdb=" O ILE H 28 " pdb="HD22 ASN H 32 " model vdw 1.704 2.450 nonbonded pdb=" O ASP A 442 " pdb="HD21 ASN A 448 " model vdw 1.715 2.450 nonbonded pdb=" HG SER A 438 " pdb=" OD2 ASP A 442 " model vdw 1.719 2.450 nonbonded pdb=" OD1 ASN A 439 " pdb=" HG SER A 443 " model vdw 1.726 2.450 nonbonded pdb="HH21 ARG L 61 " pdb=" OD1 ASP L 82 " model vdw 1.734 2.450 ... (remaining 89679 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: 3.860 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: 0.050 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.140 Find NCS groups from input model: 0.030 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 0.094 3355 Z= 0.186 Angle : 0.749 10.681 4569 Z= 0.407 Chirality : 0.047 0.191 488 Planarity : 0.005 0.077 594 Dihedral : 14.915 86.215 1201 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.16 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 12.92 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.40), residues: 411 helix: -3.27 (0.71), residues: 34 sheet: 0.05 (0.46), residues: 131 loop : -0.03 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 498 TYR 0.015 0.001 TYR A 489 PHE 0.007 0.001 PHE A 429 TRP 0.008 0.001 TRP H 105 HIS 0.002 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 3349) covalent geometry : angle 0.74704 ( 4557) SS BOND : bond 0.00898 ( 6) SS BOND : angle 1.33659 ( 12) hydrogen bonds : bond 0.22715 ( 116) hydrogen bonds : angle 9.52365 ( 291) *********************** 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 VAL 475 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Evaluate side-chains 56 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2121 time to fit residues: 13.7890 Evaluate side-chains 36 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.043865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.036459 restraints weight = 47811.127| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 4.11 r_work: 0.2707 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3355 Z= 0.138 Angle : 0.593 8.740 4569 Z= 0.306 Chirality : 0.044 0.134 488 Planarity : 0.004 0.036 594 Dihedral : 4.738 21.237 462 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.19 % Favored : 97.57 % Rotamer: Outliers : 0.84 % Allowed : 15.45 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.42), residues: 411 helix: -2.70 (0.81), residues: 34 sheet: 0.30 (0.46), residues: 124 loop : 0.14 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 24 TYR 0.011 0.001 TYR A 489 PHE 0.004 0.001 PHE A 515 TRP 0.005 0.001 TRP H 105 HIS 0.001 0.000 HIS L 31 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 3349) covalent geometry : angle 0.58754 ( 4557) SS BOND : bond 0.00488 ( 6) SS BOND : angle 1.65211 ( 12) hydrogen bonds : bond 0.04192 ( 116) hydrogen bonds : angle 6.72778 ( 291) *********************** 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 VAL 475 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Evaluate side-chains 39 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.9291 (mt-10) cc_final: 0.9051 (mt-10) REVERT: A 493 GLN cc_start: 0.9382 (mm-40) cc_final: 0.9171 (mt0) outliers start: 3 outliers final: 2 residues processed: 39 average time/residue: 0.2099 time to fit residues: 9.6576 Evaluate side-chains 34 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain L residue 13 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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 = 0.3073 r_free = 0.3073 target = 0.043880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.036599 restraints weight = 48499.682| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 4.03 r_work: 0.2720 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3355 Z= 0.120 Angle : 0.552 7.696 4569 Z= 0.280 Chirality : 0.044 0.129 488 Planarity : 0.004 0.032 594 Dihedral : 4.452 18.411 462 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.43 % Favored : 97.32 % Rotamer: Outliers : 1.97 % Allowed : 14.89 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.07 (0.42), residues: 411 helix: -2.47 (0.84), residues: 34 sheet: 0.33 (0.45), residues: 134 loop : 0.23 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.007 0.001 TYR A 489 PHE 0.004 0.001 PHE A 515 TRP 0.003 0.000 TRP H 105 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 3349) covalent geometry : angle 0.54623 ( 4557) SS BOND : bond 0.00419 ( 6) SS BOND : angle 1.59435 ( 12) hydrogen bonds : bond 0.03388 ( 116) hydrogen bonds : angle 6.06026 ( 291) *********************** 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 VAL 475 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Evaluate side-chains 44 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.9280 (mt-10) cc_final: 0.9028 (mt-10) outliers start: 7 outliers final: 2 residues processed: 44 average time/residue: 0.2072 time to fit residues: 10.6144 Evaluate side-chains 37 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain L residue 13 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 5 optimal weight: 0.0170 chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 0.0980 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.4218 ------------------------------------------------------------------------------- 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 = 0.3089 r_free = 0.3089 target = 0.044342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.037081 restraints weight = 48389.995| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 4.04 r_work: 0.2734 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3355 Z= 0.098 Angle : 0.525 7.038 4569 Z= 0.267 Chirality : 0.043 0.127 488 Planarity : 0.004 0.031 594 Dihedral : 4.155 18.136 462 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.68 % Favored : 97.08 % Rotamer: Outliers : 0.84 % Allowed : 16.01 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.03 (0.42), residues: 411 helix: -2.33 (0.85), residues: 34 sheet: 0.40 (0.45), residues: 134 loop : 0.21 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.005 0.001 TYR A 489 PHE 0.003 0.001 PHE A 515 TRP 0.003 0.000 TRP H 105 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 3349) covalent geometry : angle 0.52024 ( 4557) SS BOND : bond 0.00371 ( 6) SS BOND : angle 1.46866 ( 12) hydrogen bonds : bond 0.02923 ( 116) hydrogen bonds : angle 5.72299 ( 291) *********************** 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 VAL 475 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Evaluate side-chains 39 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.9281 (mt-10) cc_final: 0.9020 (mt-10) outliers start: 3 outliers final: 3 residues processed: 39 average time/residue: 0.2048 time to fit residues: 9.3514 Evaluate side-chains 35 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain L residue 13 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 32 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3082 r_free = 0.3082 target = 0.044118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.036796 restraints weight = 49415.115| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 4.07 r_work: 0.2724 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 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 0.037 3355 Z= 0.122 Angle : 0.528 7.125 4569 Z= 0.268 Chirality : 0.043 0.124 488 Planarity : 0.004 0.031 594 Dihedral : 4.116 18.547 462 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.41 % Favored : 96.35 % Rotamer: Outliers : 0.84 % Allowed : 15.45 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.41), residues: 411 helix: -2.09 (0.88), residues: 34 sheet: 0.37 (0.45), residues: 134 loop : 0.16 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.005 0.001 TYR H 33 PHE 0.003 0.000 PHE A 371 TRP 0.003 0.000 TRP H 105 HIS 0.001 0.000 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 3349) covalent geometry : angle 0.52280 ( 4557) SS BOND : bond 0.00399 ( 6) SS BOND : angle 1.58576 ( 12) hydrogen bonds : bond 0.02807 ( 116) hydrogen bonds : angle 5.57908 ( 291) *********************** 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 VAL 475 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Evaluate side-chains 36 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.9271 (mt-10) cc_final: 0.9021 (mt-10) outliers start: 3 outliers final: 3 residues processed: 36 average time/residue: 0.1999 time to fit residues: 8.4430 Evaluate side-chains 34 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain L residue 13 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3083 r_free = 0.3083 target = 0.044078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.036877 restraints weight = 48289.249| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 4.01 r_work: 0.2729 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3355 Z= 0.125 Angle : 0.520 7.107 4569 Z= 0.265 Chirality : 0.043 0.124 488 Planarity : 0.004 0.031 594 Dihedral : 4.105 18.281 462 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.41 % Favored : 96.35 % Rotamer: Outliers : 1.69 % Allowed : 14.89 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.41), residues: 411 helix: -1.94 (0.90), residues: 34 sheet: 0.32 (0.44), residues: 134 loop : 0.12 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.006 0.001 TYR H 33 PHE 0.004 0.000 PHE A 371 TRP 0.004 0.001 TRP H 105 HIS 0.001 0.000 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 3349) covalent geometry : angle 0.51392 ( 4557) SS BOND : bond 0.00380 ( 6) SS BOND : angle 1.57805 ( 12) hydrogen bonds : bond 0.02734 ( 116) hydrogen bonds : angle 5.53655 ( 291) *********************** 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 VAL 475 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Evaluate side-chains 38 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.9258 (mt-10) cc_final: 0.9008 (mt-10) outliers start: 6 outliers final: 5 residues processed: 37 average time/residue: 0.1898 time to fit residues: 8.2456 Evaluate side-chains 35 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.3059 r_free = 0.3059 target = 0.043317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.036086 restraints weight = 48799.232| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 4.03 r_work: 0.2697 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3355 Z= 0.165 Angle : 0.530 7.491 4569 Z= 0.272 Chirality : 0.042 0.124 488 Planarity : 0.004 0.031 594 Dihedral : 4.193 20.640 462 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.65 % Favored : 96.11 % Rotamer: Outliers : 2.25 % Allowed : 14.61 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.06 (0.41), residues: 411 helix: -2.31 (0.90), residues: 28 sheet: 0.33 (0.45), residues: 134 loop : 0.13 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.006 0.001 TYR A 501 PHE 0.003 0.001 PHE A 375 TRP 0.006 0.001 TRP H 105 HIS 0.002 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 3349) covalent geometry : angle 0.52376 ( 4557) SS BOND : bond 0.00400 ( 6) SS BOND : angle 1.69476 ( 12) hydrogen bonds : bond 0.02746 ( 116) hydrogen bonds : angle 5.58682 ( 291) *********************** 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 VAL 475 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Evaluate side-chains 39 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.9263 (mt-10) cc_final: 0.9036 (mt-10) outliers start: 8 outliers final: 6 residues processed: 39 average time/residue: 0.1997 time to fit residues: 9.2721 Evaluate side-chains 36 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 = 0.3062 r_free = 0.3062 target = 0.043426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.036174 restraints weight = 48586.895| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 4.02 r_work: 0.2708 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3355 Z= 0.145 Angle : 0.532 7.330 4569 Z= 0.273 Chirality : 0.043 0.127 488 Planarity : 0.004 0.032 594 Dihedral : 4.164 20.664 462 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.41 % Favored : 96.35 % Rotamer: Outliers : 1.69 % Allowed : 15.17 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.09 (0.41), residues: 411 helix: -2.17 (0.90), residues: 28 sheet: 0.33 (0.45), residues: 134 loop : 0.08 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.006 0.001 TYR H 33 PHE 0.003 0.001 PHE A 375 TRP 0.004 0.001 TRP H 105 HIS 0.001 0.000 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 3349) covalent geometry : angle 0.52552 ( 4557) SS BOND : bond 0.00385 ( 6) SS BOND : angle 1.64486 ( 12) hydrogen bonds : bond 0.02687 ( 116) hydrogen bonds : angle 5.52339 ( 291) *********************** 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 VAL 475 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Evaluate side-chains 37 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.9260 (mt-10) cc_final: 0.9008 (mt-10) outliers start: 6 outliers final: 6 residues processed: 37 average time/residue: 0.2107 time to fit residues: 9.1684 Evaluate side-chains 35 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3083 r_free = 0.3083 target = 0.044208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.036761 restraints weight = 47505.017| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 4.10 r_work: 0.2722 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 3355 Z= 0.142 Angle : 0.566 7.123 4569 Z= 0.288 Chirality : 0.043 0.126 488 Planarity : 0.004 0.032 594 Dihedral : 4.143 19.250 462 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.65 % Favored : 96.11 % Rotamer: Outliers : 1.97 % Allowed : 15.45 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.41), residues: 411 helix: -2.04 (0.92), residues: 28 sheet: 0.33 (0.44), residues: 134 loop : 0.06 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.005 0.001 TYR H 33 PHE 0.006 0.001 PHE H 67 TRP 0.004 0.001 TRP H 105 HIS 0.001 0.000 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 3349) covalent geometry : angle 0.55282 ( 4557) SS BOND : bond 0.01329 ( 6) SS BOND : angle 2.45865 ( 12) hydrogen bonds : bond 0.02656 ( 116) hydrogen bonds : angle 5.45630 ( 291) *********************** 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 VAL 475 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Evaluate side-chains 38 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.9265 (mt-10) cc_final: 0.9011 (mt-10) outliers start: 7 outliers final: 6 residues processed: 38 average time/residue: 0.2117 time to fit residues: 9.4995 Evaluate side-chains 37 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3086 r_free = 0.3086 target = 0.044179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.036783 restraints weight = 46889.454| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 4.06 r_work: 0.2728 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3355 Z= 0.132 Angle : 0.619 12.335 4569 Z= 0.312 Chirality : 0.045 0.197 488 Planarity : 0.004 0.040 594 Dihedral : 4.375 27.977 462 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.89 % Favored : 95.86 % Rotamer: Outliers : 1.69 % Allowed : 16.29 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.41), residues: 411 helix: -1.97 (0.93), residues: 28 sheet: 0.36 (0.44), residues: 134 loop : 0.01 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.005 0.001 TYR H 94 PHE 0.006 0.001 PHE A 392 TRP 0.003 0.000 TRP H 105 HIS 0.001 0.000 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 3349) covalent geometry : angle 0.60155 ( 4557) SS BOND : bond 0.01139 ( 6) SS BOND : angle 2.90712 ( 12) hydrogen bonds : bond 0.02700 ( 116) hydrogen bonds : angle 5.36831 ( 291) ********************** 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 VAL 475 is missing expected H atoms. Skipping. Residue VAL 71 is missing expected H atoms. Skipping. Evaluate side-chains 37 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 406 GLU cc_start: 0.9268 (mt-10) cc_final: 0.9002 (mt-10) outliers start: 6 outliers final: 6 residues processed: 37 average time/residue: 0.1889 time to fit residues: 8.3471 Evaluate side-chains 35 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 0.0570 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 = 0.3096 r_free = 0.3096 target = 0.044558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.037100 restraints weight = 46714.997| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 4.05 r_work: 0.2737 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3355 Z= 0.120 Angle : 0.616 9.971 4569 Z= 0.308 Chirality : 0.044 0.155 488 Planarity : 0.004 0.049 594 Dihedral : 4.350 30.995 462 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.14 % Favored : 95.62 % Rotamer: Outliers : 1.69 % Allowed : 16.01 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % 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: -0.18 (0.41), residues: 411 helix: -1.87 (0.95), residues: 28 sheet: 0.39 (0.45), residues: 132 loop : -0.11 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.005 0.001 TYR H 94 PHE 0.007 0.001 PHE A 392 TRP 0.003 0.000 TRP H 105 HIS 0.001 0.000 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 3349) covalent geometry : angle 0.59453 ( 4557) SS BOND : bond 0.00749 ( 6) SS BOND : angle 3.18908 ( 12) hydrogen bonds : bond 0.02766 ( 116) hydrogen bonds : angle 5.30559 ( 291) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2154.87 seconds wall clock time: 37 minutes 16.96 seconds (2236.96 seconds total)