Starting phenix.real_space_refine on Thu Jul 24 15:09:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cfh_45546/07_2025/9cfh_45546.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cfh_45546/07_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_45546/07_2025/9cfh_45546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cfh_45546/07_2025/9cfh_45546.map" model { file = "/net/cci-nas-00/data/ceres_data/9cfh_45546/07_2025/9cfh_45546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cfh_45546/07_2025/9cfh_45546.cif" } resolution = 3.1 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= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.77, per 1000 atoms: 0.90 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: 1.90 Conformation dependent library (CDL) restraints added in 650.8 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: 0.70 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: 2.76 Time building geometry restraints manager: 1.95 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: 4.730 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: 0.060 Process input model: 21.160 Find NCS groups from input model: 0.040 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.360 ------------------------------------------------------------------------------- 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 (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 (0.40), 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 TRP 0.008 0.001 TRP H 105 HIS 0.002 0.001 HIS A 339 PHE 0.007 0.001 PHE A 429 TYR 0.015 0.001 TYR A 489 ARG 0.004 0.001 ARG A 498 Details of bonding type rmsd hydrogen bonds : bond 0.22715 ( 116) hydrogen bonds : angle 9.52365 ( 291) SS BOND : bond 0.00898 ( 6) SS BOND : angle 1.33659 ( 12) covalent geometry : bond 0.00442 ( 3349) covalent geometry : angle 0.74704 ( 4557) *********************** 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 : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.4330 time to fit residues: 28.3643 Evaluate side-chains 34 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 chunk 31 optimal weight: 0.0870 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.044414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.036983 restraints weight = 47320.515| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 4.07 r_work: 0.2723 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3355 Z= 0.123 Angle : 0.602 8.602 4569 Z= 0.309 Chirality : 0.045 0.135 488 Planarity : 0.004 0.035 594 Dihedral : 4.705 19.861 462 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.19 % Favored : 97.57 % Rotamer: Outliers : 1.12 % Allowed : 15.17 % 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 (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: -2.66 (0.82), residues: 34 sheet: 0.32 (0.46), residues: 124 loop : 0.17 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 105 HIS 0.001 0.000 HIS L 31 PHE 0.005 0.001 PHE A 377 TYR 0.010 0.001 TYR A 489 ARG 0.005 0.001 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.03942 ( 116) hydrogen bonds : angle 6.60635 ( 291) SS BOND : bond 0.00711 ( 6) SS BOND : angle 2.38859 ( 12) covalent geometry : bond 0.00288 ( 3349) covalent geometry : angle 0.59004 ( 4557) *********************** 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 42 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.9325 (mt-10) cc_final: 0.9063 (mt-10) REVERT: A 493 GLN cc_start: 0.9374 (mm-40) cc_final: 0.9167 (mt0) outliers start: 4 outliers final: 2 residues processed: 42 average time/residue: 0.4253 time to fit residues: 21.1541 Evaluate side-chains 35 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 15 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3076 r_free = 0.3076 target = 0.044132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.036868 restraints weight = 47807.224| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 3.99 r_work: 0.2727 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 3355 Z= 0.131 Angle : 0.582 7.777 4569 Z= 0.292 Chirality : 0.043 0.128 488 Planarity : 0.004 0.035 594 Dihedral : 4.583 28.207 462 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.92 % Favored : 96.84 % 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 (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: -0.04 (0.42), residues: 411 helix: -2.32 (0.86), residues: 34 sheet: 0.35 (0.45), residues: 134 loop : 0.23 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP H 105 HIS 0.001 0.000 HIS A 519 PHE 0.014 0.001 PHE A 338 TYR 0.007 0.001 TYR A 489 ARG 0.003 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.03434 ( 116) hydrogen bonds : angle 6.13077 ( 291) SS BOND : bond 0.01166 ( 6) SS BOND : angle 2.02955 ( 12) covalent geometry : bond 0.00307 ( 3349) covalent geometry : angle 0.57320 ( 4557) *********************** 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 41 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.9281 (mt-10) cc_final: 0.9034 (mt-10) outliers start: 6 outliers final: 2 residues processed: 41 average time/residue: 0.4290 time to fit residues: 21.0365 Evaluate side-chains 36 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 3 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.0870 chunk 11 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- 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 = 0.3071 r_free = 0.3071 target = 0.043891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.036437 restraints weight = 48860.852| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 4.09 r_work: 0.2712 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3355 Z= 0.140 Angle : 0.540 7.501 4569 Z= 0.276 Chirality : 0.043 0.125 488 Planarity : 0.004 0.031 594 Dihedral : 4.308 18.946 462 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.92 % Favored : 96.84 % Rotamer: Outliers : 0.84 % Allowed : 15.73 % 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 (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: -0.01 (0.41), residues: 411 helix: -2.57 (0.92), residues: 28 sheet: 0.40 (0.45), residues: 134 loop : 0.20 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 105 HIS 0.002 0.000 HIS A 339 PHE 0.012 0.001 PHE A 338 TYR 0.007 0.001 TYR A 501 ARG 0.003 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.03050 ( 116) hydrogen bonds : angle 5.74154 ( 291) SS BOND : bond 0.00771 ( 6) SS BOND : angle 2.18928 ( 12) covalent geometry : bond 0.00323 ( 3349) covalent geometry : angle 0.52903 ( 4557) *********************** 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 38 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.9270 (mt-10) cc_final: 0.9028 (mt-10) outliers start: 3 outliers final: 3 residues processed: 38 average time/residue: 0.4413 time to fit residues: 20.1506 Evaluate side-chains 37 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 18 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3076 r_free = 0.3076 target = 0.044127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.036727 restraints weight = 48344.666| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 4.07 r_work: 0.2716 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3111 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= 0.132 Angle : 0.567 10.936 4569 Z= 0.287 Chirality : 0.043 0.156 488 Planarity : 0.004 0.051 594 Dihedral : 4.448 28.661 462 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.16 % Favored : 96.59 % Rotamer: Outliers : 1.69 % Allowed : 14.61 % 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 (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: -0.01 (0.41), residues: 411 helix: -2.43 (0.92), residues: 28 sheet: 0.39 (0.45), residues: 132 loop : 0.18 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP H 105 HIS 0.001 0.000 HIS A 519 PHE 0.007 0.001 PHE A 392 TYR 0.006 0.001 TYR H 33 ARG 0.003 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.02993 ( 116) hydrogen bonds : angle 5.67979 ( 291) SS BOND : bond 0.01048 ( 6) SS BOND : angle 1.74926 ( 12) covalent geometry : bond 0.00305 ( 3349) covalent geometry : angle 0.56062 ( 4557) *********************** 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 42 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.9272 (mt-10) cc_final: 0.9030 (mt-10) outliers start: 6 outliers final: 5 residues processed: 42 average time/residue: 0.4183 time to fit residues: 21.0652 Evaluate side-chains 38 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3076 r_free = 0.3076 target = 0.043984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.036728 restraints weight = 48186.999| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 4.03 r_work: 0.2721 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 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 0.037 3355 Z= 0.126 Angle : 0.543 8.303 4569 Z= 0.278 Chirality : 0.043 0.133 488 Planarity : 0.004 0.055 594 Dihedral : 4.370 22.237 462 Min Nonbonded Distance : 2.478 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 (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: -0.02 (0.41), residues: 411 helix: -1.92 (0.88), residues: 34 sheet: 0.29 (0.44), residues: 134 loop : 0.22 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 105 HIS 0.001 0.000 HIS A 339 PHE 0.003 0.000 PHE A 455 TYR 0.006 0.001 TYR H 94 ARG 0.003 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.02849 ( 116) hydrogen bonds : angle 5.49548 ( 291) SS BOND : bond 0.00534 ( 6) SS BOND : angle 1.83709 ( 12) covalent geometry : bond 0.00294 ( 3349) covalent geometry : angle 0.53499 ( 4557) *********************** 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 : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.9282 (mt-10) cc_final: 0.9041 (mt-10) outliers start: 6 outliers final: 5 residues processed: 37 average time/residue: 0.3971 time to fit residues: 17.6305 Evaluate side-chains 34 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 14 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3081 r_free = 0.3081 target = 0.044171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.036878 restraints weight = 48895.029| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 4.05 r_work: 0.2725 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3440 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= 0.116 Angle : 0.546 7.070 4569 Z= 0.280 Chirality : 0.043 0.126 488 Planarity : 0.004 0.050 594 Dihedral : 4.303 26.777 462 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.41 % Favored : 96.35 % Rotamer: Outliers : 2.25 % Allowed : 14.33 % 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 (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: -0.00 (0.42), residues: 411 helix: -2.10 (0.95), residues: 28 sheet: 0.37 (0.45), residues: 134 loop : 0.16 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 105 HIS 0.001 0.000 HIS A 519 PHE 0.003 0.001 PHE A 392 TYR 0.006 0.001 TYR H 33 ARG 0.004 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.02783 ( 116) hydrogen bonds : angle 5.48990 ( 291) SS BOND : bond 0.00396 ( 6) SS BOND : angle 2.49883 ( 12) covalent geometry : bond 0.00274 ( 3349) covalent geometry : angle 0.53183 ( 4557) *********************** 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 38 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.9286 (mt-10) cc_final: 0.9042 (mt-10) outliers start: 8 outliers final: 6 residues processed: 37 average time/residue: 0.4139 time to fit residues: 18.3469 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 : 0.582 ------------------------------------------------------------------------------- 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 H residue 2 VAL 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 28 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3078 r_free = 0.3078 target = 0.044100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.036751 restraints weight = 49058.586| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 4.06 r_work: 0.2721 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3552 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= 0.126 Angle : 0.536 6.976 4569 Z= 0.275 Chirality : 0.043 0.126 488 Planarity : 0.004 0.052 594 Dihedral : 4.173 21.630 462 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.89 % Favored : 95.86 % 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 (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: -0.02 (0.41), residues: 411 helix: -1.93 (0.97), residues: 28 sheet: 0.37 (0.45), residues: 134 loop : 0.11 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 105 HIS 0.001 0.000 HIS A 339 PHE 0.003 0.000 PHE A 375 TYR 0.006 0.001 TYR H 94 ARG 0.004 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.02729 ( 116) hydrogen bonds : angle 5.37459 ( 291) SS BOND : bond 0.00435 ( 6) SS BOND : angle 2.12457 ( 12) covalent geometry : bond 0.00295 ( 3349) covalent geometry : angle 0.52561 ( 4557) *********************** 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 36 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.9287 (mt-10) cc_final: 0.9042 (mt-10) REVERT: L 68 GLU cc_start: 0.9186 (mp0) cc_final: 0.8965 (mp0) outliers start: 7 outliers final: 6 residues processed: 35 average time/residue: 0.4022 time to fit residues: 17.0004 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 : 0.529 ------------------------------------------------------------------------------- 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 H residue 2 VAL 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 23 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.0470 chunk 21 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- 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 = 0.044236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.036960 restraints weight = 48450.947| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 4.04 r_work: 0.2733 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3691 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= 0.110 Angle : 0.528 6.798 4569 Z= 0.270 Chirality : 0.043 0.127 488 Planarity : 0.004 0.039 594 Dihedral : 4.019 18.148 462 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.89 % Favored : 95.86 % 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 (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: -0.06 (0.41), residues: 411 helix: -1.63 (0.91), residues: 34 sheet: 0.40 (0.45), residues: 134 loop : 0.05 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP H 105 HIS 0.001 0.000 HIS A 339 PHE 0.003 0.000 PHE A 455 TYR 0.005 0.001 TYR H 94 ARG 0.003 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.02653 ( 116) hydrogen bonds : angle 5.25987 ( 291) SS BOND : bond 0.00369 ( 6) SS BOND : angle 1.86210 ( 12) covalent geometry : bond 0.00265 ( 3349) covalent geometry : angle 0.52027 ( 4557) *********************** 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 35 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.9299 (mt-10) cc_final: 0.9047 (mt-10) outliers start: 7 outliers final: 7 residues processed: 34 average time/residue: 0.4006 time to fit residues: 16.3380 Evaluate side-chains 35 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain H residue 2 VAL 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 16 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.044179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.036866 restraints weight = 48396.931| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 4.03 r_work: 0.2726 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3355 Z= 0.120 Angle : 0.524 6.875 4569 Z= 0.268 Chirality : 0.043 0.126 488 Planarity : 0.004 0.039 594 Dihedral : 4.002 18.488 462 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.89 % Favored : 95.86 % 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 (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: -0.01 (0.41), residues: 411 helix: -1.73 (0.99), residues: 28 sheet: 0.44 (0.45), residues: 134 loop : 0.04 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP H 105 HIS 0.001 0.000 HIS A 339 PHE 0.006 0.001 PHE H 67 TYR 0.006 0.001 TYR H 94 ARG 0.004 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.02606 ( 116) hydrogen bonds : angle 5.21794 ( 291) SS BOND : bond 0.00435 ( 6) SS BOND : angle 1.77416 ( 12) covalent geometry : bond 0.00282 ( 3349) covalent geometry : angle 0.51702 ( 4557) ********************** 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 34 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.9294 (mt-10) cc_final: 0.9037 (mt-10) outliers start: 6 outliers final: 6 residues processed: 33 average time/residue: 0.4083 time to fit residues: 16.2204 Evaluate side-chains 34 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 H residue 2 VAL 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 24 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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 = 0.3074 r_free = 0.3074 target = 0.043933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.036552 restraints weight = 49669.937| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 4.08 r_work: 0.2714 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.3780 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= 0.142 Angle : 0.536 7.126 4569 Z= 0.274 Chirality : 0.042 0.126 488 Planarity : 0.004 0.032 594 Dihedral : 4.057 18.611 462 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.14 % Favored : 95.62 % Rotamer: Outliers : 1.69 % Allowed : 15.45 % Favored : 82.87 % 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: -0.02 (0.41), residues: 411 helix: -1.63 (1.00), residues: 28 sheet: 0.50 (0.45), residues: 134 loop : -0.01 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 105 HIS 0.002 0.001 HIS A 339 PHE 0.007 0.001 PHE A 374 TYR 0.006 0.001 TYR H 94 ARG 0.004 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.02624 ( 116) hydrogen bonds : angle 5.23283 ( 291) SS BOND : bond 0.00454 ( 6) SS BOND : angle 1.77485 ( 12) covalent geometry : bond 0.00325 ( 3349) covalent geometry : angle 0.52875 ( 4557) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5004.95 seconds wall clock time: 88 minutes 27.44 seconds (5307.44 seconds total)