Starting phenix.real_space_refine on Wed Mar 5 18:42:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvf_34125/03_2025/7yvf_34125.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvf_34125/03_2025/7yvf_34125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yvf_34125/03_2025/7yvf_34125.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvf_34125/03_2025/7yvf_34125.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvf_34125/03_2025/7yvf_34125.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvf_34125/03_2025/7yvf_34125.cif" } resolution = 3.4 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= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2094 2.51 5 N 562 2.21 5 O 613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3283 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "C" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 956 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "B" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1511 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 11, 'TRANS': 181} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 3.65, per 1000 atoms: 1.11 Number of scatterers: 3283 At special positions: 0 Unit cell: (74.62, 90.2, 84.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 613 8.00 N 562 7.00 C 2094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 97 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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: 0.68 Conformation dependent library (CDL) restraints added in 363.3 milliseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 778 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 7 sheets defined 13.4% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.943A pdb=" N ASP A 83 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU A 84 " --> pdb=" O SER A 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 80 through 84' Processing helix chain 'C' and resid 63 through 66 Processing helix chain 'C' and resid 88 through 92 removed outlier: 3.593A pdb=" N THR C 92 " --> pdb=" O PRO C 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.913A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.616A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.227A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.529A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.932A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.565A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 49 removed outlier: 6.629A pdb=" N TRP A 36 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 8 Processing sheet with id=AA4, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.566A pdb=" N ALA C 51 " --> pdb=" O TRP C 38 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ARG C 40 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N TRP C 49 " --> pdb=" O ARG C 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA6, first strand: chain 'B' and resid 391 through 392 removed outlier: 3.650A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 100 hydrogen bonds defined for protein. 228 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.74 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1053 1.34 - 1.46: 902 1.46 - 1.58: 1403 1.58 - 1.70: 0 1.70 - 1.82: 16 Bond restraints: 3374 Sorted by residual: bond pdb=" C HIS B 505 " pdb=" N GLN B 506 " ideal model delta sigma weight residual 1.340 1.262 0.078 5.87e-02 2.90e+02 1.77e+00 bond pdb=" C HIS C 104 " pdb=" N ASN C 105 " ideal model delta sigma weight residual 1.331 1.303 0.028 2.22e-02 2.03e+03 1.55e+00 bond pdb=" CD2 TYR B 495 " pdb=" CE2 TYR B 495 " ideal model delta sigma weight residual 1.382 1.345 0.037 3.00e-02 1.11e+03 1.53e+00 bond pdb=" CG1 ILE B 472 " pdb=" CD1 ILE B 472 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.31e+00 bond pdb=" N CYS B 488 " pdb=" CA CYS B 488 " ideal model delta sigma weight residual 1.457 1.472 -0.014 1.29e-02 6.01e+03 1.22e+00 ... (remaining 3369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 4323 1.42 - 2.83: 225 2.83 - 4.25: 40 4.25 - 5.67: 9 5.67 - 7.08: 3 Bond angle restraints: 4600 Sorted by residual: angle pdb=" CA CYS B 488 " pdb=" CB CYS B 488 " pdb=" SG CYS B 488 " ideal model delta sigma weight residual 114.40 121.25 -6.85 2.30e+00 1.89e-01 8.87e+00 angle pdb=" C SER A 51 " pdb=" N ASN A 52 " pdb=" CA ASN A 52 " ideal model delta sigma weight residual 121.54 127.17 -5.63 1.91e+00 2.74e-01 8.68e+00 angle pdb=" N PRO B 521 " pdb=" CA PRO B 521 " pdb=" C PRO B 521 " ideal model delta sigma weight residual 112.92 105.84 7.08 2.73e+00 1.34e-01 6.73e+00 angle pdb=" N ASN B 477 " pdb=" CA ASN B 477 " pdb=" C ASN B 477 " ideal model delta sigma weight residual 110.14 106.19 3.95 1.55e+00 4.16e-01 6.49e+00 angle pdb=" C ASN B 487 " pdb=" N CYS B 488 " pdb=" CA CYS B 488 " ideal model delta sigma weight residual 121.54 126.30 -4.76 1.91e+00 2.74e-01 6.21e+00 ... (remaining 4595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.83: 1648 11.83 - 23.66: 224 23.66 - 35.48: 76 35.48 - 47.31: 17 47.31 - 59.14: 8 Dihedral angle restraints: 1973 sinusoidal: 750 harmonic: 1223 Sorted by residual: dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 89 " pdb=" CB CYS A 89 " ideal model delta sinusoidal sigma weight residual 93.00 149.96 -56.96 1 1.00e+01 1.00e-02 4.37e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 39.96 53.04 1 1.00e+01 1.00e-02 3.83e+01 dihedral pdb=" CA ALA B 520 " pdb=" C ALA B 520 " pdb=" N PRO B 521 " pdb=" CA PRO B 521 " ideal model delta harmonic sigma weight residual 180.00 158.76 21.24 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 1970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 303 0.038 - 0.077: 139 0.077 - 0.115: 44 0.115 - 0.154: 12 0.154 - 0.192: 2 Chirality restraints: 500 Sorted by residual: chirality pdb=" CB THR C 106 " pdb=" CA THR C 106 " pdb=" OG1 THR C 106 " pdb=" CG2 THR C 106 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.21e-01 chirality pdb=" CA PRO B 491 " pdb=" N PRO B 491 " pdb=" C PRO B 491 " pdb=" CB PRO B 491 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.20e-01 chirality pdb=" CA THR C 15 " pdb=" N THR C 15 " pdb=" C THR C 15 " pdb=" CB THR C 15 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 497 not shown) Planarity restraints: 594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 495 " 0.012 2.00e-02 2.50e+03 2.07e-02 8.55e+00 pdb=" CG TYR B 495 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR B 495 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR B 495 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B 495 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 495 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 495 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR B 495 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 35 " -0.013 2.00e-02 2.50e+03 2.70e-02 7.28e+00 pdb=" C TYR A 35 " 0.047 2.00e-02 2.50e+03 pdb=" O TYR A 35 " -0.018 2.00e-02 2.50e+03 pdb=" N TRP A 36 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 53 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.85e+00 pdb=" C ILE C 53 " -0.045 2.00e-02 2.50e+03 pdb=" O ILE C 53 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR C 54 " 0.015 2.00e-02 2.50e+03 ... (remaining 591 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 514 2.75 - 3.29: 2931 3.29 - 3.83: 4949 3.83 - 4.36: 6045 4.36 - 4.90: 10813 Nonbonded interactions: 25252 Sorted by model distance: nonbonded pdb=" O VAL B 367 " pdb=" ND2 ASN B 370 " model vdw 2.217 3.120 nonbonded pdb=" O GLY C 33 " pdb=" NH1 ARG C 100 " model vdw 2.253 3.120 nonbonded pdb=" NH1 ARG B 457 " pdb=" O SER B 459 " model vdw 2.257 3.120 nonbonded pdb=" O TRP B 353 " pdb=" NH1 ARG B 466 " model vdw 2.306 3.120 nonbonded pdb=" O ARG C 66 " pdb=" OG SER C 67 " model vdw 2.334 3.040 ... (remaining 25247 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: 5.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.080 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 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 : 0.006 0.078 3374 Z= 0.382 Angle : 0.755 7.082 4600 Z= 0.419 Chirality : 0.049 0.192 500 Planarity : 0.006 0.043 594 Dihedral : 12.395 59.137 1177 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.64 % Favored : 91.89 % Rotamer: Outliers : 0.56 % Allowed : 5.08 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.93 (0.35), residues: 419 helix: -4.76 (0.45), residues: 28 sheet: -1.73 (0.40), residues: 158 loop : -3.05 (0.33), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 55 HIS 0.006 0.002 HIS C 99 PHE 0.017 0.001 PHE B 392 TYR 0.050 0.002 TYR B 495 ARG 0.002 0.000 ARG C 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.367 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 88 average time/residue: 0.2472 time to fit residues: 25.1190 Evaluate side-chains 62 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 495 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 54 GLN C 78 ASN C 86 ASN C 99 HIS B 370 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.086939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.075273 restraints weight = 7470.947| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.55 r_work: 0.2929 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3374 Z= 0.225 Angle : 0.633 7.828 4600 Z= 0.327 Chirality : 0.046 0.151 500 Planarity : 0.005 0.037 594 Dihedral : 5.632 33.525 468 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.77 % Favored : 94.99 % Rotamer: Outliers : 2.54 % Allowed : 17.23 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -3.13 (0.36), residues: 419 helix: -5.04 (0.21), residues: 28 sheet: -1.12 (0.40), residues: 153 loop : -2.42 (0.35), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 55 HIS 0.004 0.001 HIS A 50 PHE 0.014 0.001 PHE B 375 TYR 0.006 0.001 TYR B 453 ARG 0.005 0.000 ARG B 452 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.303 Fit side-chains REVERT: B 418 ILE cc_start: 0.9351 (pt) cc_final: 0.8982 (mt) REVERT: B 420 ASP cc_start: 0.8527 (t0) cc_final: 0.7917 (t0) outliers start: 9 outliers final: 4 residues processed: 78 average time/residue: 0.1790 time to fit residues: 16.4569 Evaluate side-chains 67 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 108 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- 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 = 0.3170 r_free = 0.3170 target = 0.083180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.071853 restraints weight = 7474.072| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.50 r_work: 0.2874 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 3374 Z= 0.441 Angle : 0.731 9.336 4600 Z= 0.380 Chirality : 0.049 0.173 500 Planarity : 0.005 0.042 594 Dihedral : 5.790 35.031 466 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.52 % Allowed : 17.80 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.88 (0.37), residues: 419 helix: -4.90 (0.33), residues: 28 sheet: -0.91 (0.39), residues: 158 loop : -2.29 (0.35), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 99 HIS 0.004 0.002 HIS C 104 PHE 0.011 0.001 PHE B 375 TYR 0.011 0.001 TYR B 453 ARG 0.006 0.001 ARG B 452 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.354 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 76 average time/residue: 0.1647 time to fit residues: 15.0789 Evaluate side-chains 70 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3215 r_free = 0.3215 target = 0.085627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.074106 restraints weight = 7656.071| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.59 r_work: 0.2914 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3374 Z= 0.225 Angle : 0.650 9.469 4600 Z= 0.324 Chirality : 0.046 0.149 500 Planarity : 0.005 0.037 594 Dihedral : 5.321 35.868 466 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 4.24 % Allowed : 20.06 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.44 (0.37), residues: 419 helix: -4.91 (0.32), residues: 28 sheet: -0.54 (0.40), residues: 152 loop : -1.98 (0.36), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.003 0.001 HIS A 38 PHE 0.010 0.001 PHE B 375 TYR 0.008 0.001 TYR B 489 ARG 0.004 0.000 ARG B 452 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.291 Fit side-chains REVERT: B 418 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.9075 (mt) outliers start: 15 outliers final: 9 residues processed: 76 average time/residue: 0.1858 time to fit residues: 16.8465 Evaluate side-chains 70 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 511 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.0670 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.7920 ------------------------------------------------------------------------------- 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 = 0.3221 r_free = 0.3221 target = 0.086043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.074587 restraints weight = 7672.981| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.59 r_work: 0.2924 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3374 Z= 0.215 Angle : 0.638 10.170 4600 Z= 0.317 Chirality : 0.046 0.147 500 Planarity : 0.004 0.034 594 Dihedral : 5.180 35.577 466 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.80 % Allowed : 19.77 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.21 (0.38), residues: 419 helix: -4.83 (0.41), residues: 28 sheet: -0.28 (0.41), residues: 150 loop : -1.88 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.002 0.001 HIS A 38 PHE 0.010 0.001 PHE B 400 TYR 0.006 0.001 TYR C 96 ARG 0.003 0.000 ARG B 452 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.387 Fit side-chains REVERT: B 418 ILE cc_start: 0.9349 (pt) cc_final: 0.9084 (mt) outliers start: 17 outliers final: 13 residues processed: 77 average time/residue: 0.1611 time to fit residues: 15.0709 Evaluate side-chains 73 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3235 r_free = 0.3235 target = 0.086734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.075335 restraints weight = 7663.997| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.60 r_work: 0.2937 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3374 Z= 0.229 Angle : 0.645 10.838 4600 Z= 0.320 Chirality : 0.045 0.147 500 Planarity : 0.004 0.032 594 Dihedral : 5.128 35.244 466 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.80 % Allowed : 20.06 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.07 (0.38), residues: 419 helix: -4.77 (0.47), residues: 28 sheet: -0.20 (0.41), residues: 152 loop : -1.78 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 436 HIS 0.002 0.001 HIS A 38 PHE 0.010 0.001 PHE B 400 TYR 0.007 0.001 TYR C 96 ARG 0.003 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.366 Fit side-chains REVERT: B 418 ILE cc_start: 0.9362 (pt) cc_final: 0.9132 (mt) outliers start: 17 outliers final: 14 residues processed: 77 average time/residue: 0.1584 time to fit residues: 14.8491 Evaluate side-chains 74 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.0870 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 = 0.3248 r_free = 0.3248 target = 0.087526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.076198 restraints weight = 7484.134| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.56 r_work: 0.2952 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3374 Z= 0.201 Angle : 0.642 10.896 4600 Z= 0.315 Chirality : 0.045 0.150 500 Planarity : 0.004 0.031 594 Dihedral : 5.026 34.922 466 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 5.37 % Allowed : 21.19 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.93 (0.39), residues: 419 helix: -4.75 (0.48), residues: 28 sheet: -0.15 (0.41), residues: 152 loop : -1.63 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.002 0.001 HIS A 38 PHE 0.010 0.001 PHE B 400 TYR 0.006 0.001 TYR C 96 ARG 0.003 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.377 Fit side-chains outliers start: 19 outliers final: 15 residues processed: 78 average time/residue: 0.1474 time to fit residues: 14.1718 Evaluate side-chains 78 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3247 r_free = 0.3247 target = 0.087383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.076015 restraints weight = 7540.907| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.55 r_work: 0.2953 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3374 Z= 0.214 Angle : 0.647 11.214 4600 Z= 0.318 Chirality : 0.045 0.152 500 Planarity : 0.004 0.030 594 Dihedral : 5.002 34.406 466 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 5.08 % Allowed : 21.75 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.85 (0.39), residues: 419 helix: -4.74 (0.49), residues: 28 sheet: -0.13 (0.41), residues: 157 loop : -1.56 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 436 HIS 0.003 0.001 HIS A 38 PHE 0.009 0.001 PHE B 400 TYR 0.007 0.001 TYR C 96 ARG 0.004 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.368 Fit side-chains outliers start: 18 outliers final: 15 residues processed: 79 average time/residue: 0.1627 time to fit residues: 15.7969 Evaluate side-chains 77 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3236 r_free = 0.3236 target = 0.086853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.075527 restraints weight = 7435.576| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.52 r_work: 0.2943 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3374 Z= 0.251 Angle : 0.678 11.393 4600 Z= 0.332 Chirality : 0.046 0.170 500 Planarity : 0.005 0.032 594 Dihedral : 5.149 35.100 466 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 4.80 % Allowed : 22.32 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.84 (0.39), residues: 419 helix: -4.77 (0.49), residues: 29 sheet: -0.16 (0.41), residues: 159 loop : -1.52 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 99 HIS 0.003 0.001 HIS A 38 PHE 0.009 0.001 PHE B 400 TYR 0.008 0.001 TYR C 96 ARG 0.005 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.377 Fit side-chains outliers start: 17 outliers final: 15 residues processed: 76 average time/residue: 0.1498 time to fit residues: 14.2123 Evaluate side-chains 76 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 40 optimal weight: 0.0170 chunk 19 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 = 0.3270 r_free = 0.3270 target = 0.088858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.077438 restraints weight = 7465.307| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.54 r_work: 0.2975 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3374 Z= 0.188 Angle : 0.666 12.932 4600 Z= 0.322 Chirality : 0.045 0.154 500 Planarity : 0.004 0.031 594 Dihedral : 4.879 34.263 466 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.82 % Allowed : 25.14 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.72 (0.39), residues: 419 helix: -4.78 (0.48), residues: 29 sheet: 0.02 (0.42), residues: 152 loop : -1.46 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.002 0.001 HIS A 38 PHE 0.009 0.001 PHE B 400 TYR 0.007 0.001 TYR B 351 ARG 0.006 0.000 ARG C 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.364 Fit side-chains REVERT: B 420 ASP cc_start: 0.8403 (t0) cc_final: 0.7824 (t0) REVERT: B 489 TYR cc_start: 0.5744 (m-10) cc_final: 0.5501 (m-10) outliers start: 10 outliers final: 10 residues processed: 73 average time/residue: 0.1393 time to fit residues: 12.5181 Evaluate side-chains 73 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 0.0370 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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 = 0.3259 r_free = 0.3259 target = 0.088174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.076793 restraints weight = 7454.160| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.51 r_work: 0.2965 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 3374 Z= 0.242 Angle : 0.704 12.561 4600 Z= 0.341 Chirality : 0.047 0.292 500 Planarity : 0.004 0.031 594 Dihedral : 5.023 33.656 466 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 3.67 % Allowed : 24.29 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.64 (0.40), residues: 419 helix: -4.74 (0.50), residues: 28 sheet: 0.05 (0.42), residues: 154 loop : -1.42 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 436 HIS 0.003 0.001 HIS A 38 PHE 0.010 0.001 PHE B 400 TYR 0.007 0.001 TYR C 96 ARG 0.006 0.000 ARG C 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2396.67 seconds wall clock time: 41 minutes 58.64 seconds (2518.64 seconds total)