Starting phenix.real_space_refine on Mon Feb 10 23:39:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvf_34125/02_2025/7yvf_34125.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvf_34125/02_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_34125/02_2025/7yvf_34125.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvf_34125/02_2025/7yvf_34125.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvf_34125/02_2025/7yvf_34125.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvf_34125/02_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-5592/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: 4.78, per 1000 atoms: 1.46 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: 0.77 Conformation dependent library (CDL) restraints added in 416.6 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: 0.36 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: 0.75 Time building geometry restraints manager: 0.91 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: 7.810 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.610 Find NCS groups from input model: 0.040 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.610 ------------------------------------------------------------------------------- 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 : 0.372 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 88 average time/residue: 0.2357 time to fit residues: 23.7445 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 : 0.419 ------------------------------------------------------------------------------- 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 = 36)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.075273 restraints weight = 7470.947| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.55 r_work: 0.2928 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- 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 : 0.308 Fit side-chains REVERT: B 418 ILE cc_start: 0.9351 (pt) cc_final: 0.8982 (mt) REVERT: B 420 ASP cc_start: 0.8525 (t0) cc_final: 0.7916 (t0) outliers start: 9 outliers final: 4 residues processed: 78 average time/residue: 0.1791 time to fit residues: 16.4908 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 : 0.376 ------------------------------------------------------------------------------- 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: 0.8980 chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3199 r_free = 0.3199 target = 0.084760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.073306 restraints weight = 7421.794| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.53 r_work: 0.2902 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 3374 Z= 0.322 Angle : 0.673 8.833 4600 Z= 0.346 Chirality : 0.047 0.158 500 Planarity : 0.005 0.038 594 Dihedral : 5.428 34.129 466 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.95 % Allowed : 17.80 % Favored : 78.25 % 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: -2.75 (0.37), residues: 419 helix: -4.94 (0.29), residues: 28 sheet: -0.78 (0.40), residues: 157 loop : -2.22 (0.35), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 99 HIS 0.004 0.002 HIS C 104 PHE 0.011 0.001 PHE B 375 TYR 0.009 0.001 TYR B 489 ARG 0.005 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 79 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.363 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 75 average time/residue: 0.1717 time to fit residues: 15.5115 Evaluate side-chains 69 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 1 optimal weight: 0.0040 chunk 6 optimal weight: 0.0470 chunk 29 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 overall best weight: 0.4890 ------------------------------------------------------------------------------- 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 = 0.3256 r_free = 0.3256 target = 0.087830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.076131 restraints weight = 7626.371| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.57 r_work: 0.2958 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3374 Z= 0.164 Angle : 0.621 9.556 4600 Z= 0.305 Chirality : 0.045 0.145 500 Planarity : 0.004 0.035 594 Dihedral : 4.965 34.923 466 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.11 % Allowed : 20.06 % Favored : 76.84 % 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: -2.26 (0.38), residues: 419 helix: -4.93 (0.31), residues: 28 sheet: -0.32 (0.42), residues: 150 loop : -1.90 (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 0.007 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 76 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.390 Fit side-chains REVERT: B 418 ILE cc_start: 0.9312 (pt) cc_final: 0.9110 (mt) outliers start: 11 outliers final: 6 residues processed: 74 average time/residue: 0.1758 time to fit residues: 15.6106 Evaluate side-chains 67 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 LEU 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 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: 0.0270 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- 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 = 0.3253 r_free = 0.3253 target = 0.087707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.076150 restraints weight = 7602.821| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.62 r_work: 0.2953 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3374 Z= 0.204 Angle : 0.626 9.943 4600 Z= 0.310 Chirality : 0.045 0.148 500 Planarity : 0.004 0.035 594 Dihedral : 4.922 34.366 466 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 3.95 % Allowed : 19.77 % Favored : 76.27 % 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: -2.09 (0.38), residues: 419 helix: -4.81 (0.42), residues: 28 sheet: -0.18 (0.42), residues: 150 loop : -1.81 (0.36), residues: 241 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 0.010 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 79 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.353 Fit side-chains REVERT: B 418 ILE cc_start: 0.9319 (pt) cc_final: 0.9106 (mt) outliers start: 14 outliers final: 10 residues processed: 76 average time/residue: 0.1481 time to fit residues: 13.8807 Evaluate side-chains 71 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 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 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 C residue 122 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 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 = 0.3249 r_free = 0.3249 target = 0.087618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.076232 restraints weight = 7680.715| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.60 r_work: 0.2952 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2620 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= 0.210 Angle : 0.629 10.709 4600 Z= 0.311 Chirality : 0.045 0.147 500 Planarity : 0.004 0.033 594 Dihedral : 4.933 34.263 466 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 5.08 % Allowed : 18.08 % Favored : 76.84 % 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: -2.00 (0.39), residues: 419 helix: -4.76 (0.47), residues: 28 sheet: -0.19 (0.42), residues: 152 loop : -1.70 (0.37), residues: 239 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 0.006 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 78 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.396 Fit side-chains outliers start: 18 outliers final: 14 residues processed: 74 average time/residue: 0.1408 time to fit residues: 13.1110 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 : 0.394 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3206 r_free = 0.3206 target = 0.085150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.074042 restraints weight = 7564.502| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.53 r_work: 0.2913 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 3374 Z= 0.330 Angle : 0.695 11.568 4600 Z= 0.347 Chirality : 0.047 0.163 500 Planarity : 0.005 0.032 594 Dihedral : 5.341 34.261 466 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % 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: -1.97 (0.39), residues: 419 helix: -4.75 (0.49), residues: 28 sheet: -0.19 (0.41), residues: 157 loop : -1.67 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 99 HIS 0.002 0.001 HIS A 38 PHE 0.009 0.001 PHE B 377 TYR 0.009 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 79 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.354 Fit side-chains outliers start: 19 outliers final: 16 residues processed: 74 average time/residue: 0.1571 time to fit residues: 14.3501 Evaluate side-chains 76 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 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 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: 0.3980 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 0.0050 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 27 optimal weight: 0.0370 chunk 13 optimal weight: 0.5980 overall best weight: 0.3472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.089330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.077850 restraints weight = 7504.632| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.55 r_work: 0.2986 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3374 Z= 0.161 Angle : 0.637 12.338 4600 Z= 0.308 Chirality : 0.045 0.152 500 Planarity : 0.004 0.031 594 Dihedral : 4.840 34.858 466 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.95 % Allowed : 22.32 % Favored : 73.73 % 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: -1.82 (0.39), residues: 419 helix: -4.75 (0.49), residues: 28 sheet: 0.02 (0.42), residues: 149 loop : -1.61 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 B 489 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 81 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.372 Fit side-chains REVERT: B 420 ASP cc_start: 0.8466 (t0) cc_final: 0.7911 (t0) outliers start: 14 outliers final: 11 residues processed: 78 average time/residue: 0.1443 time to fit residues: 13.8144 Evaluate side-chains 72 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER 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 C residue 122 SER Chi-restraints excluded: chain B residue 440 LYS 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: 2.9990 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- 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 = 0.3199 r_free = 0.3199 target = 0.084770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.073680 restraints weight = 7537.449| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.49 r_work: 0.2903 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 3374 Z= 0.396 Angle : 0.737 11.840 4600 Z= 0.367 Chirality : 0.048 0.179 500 Planarity : 0.005 0.032 594 Dihedral : 5.491 34.481 466 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 3.95 % Allowed : 23.16 % 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: -1.99 (0.39), residues: 419 helix: -4.75 (0.49), residues: 28 sheet: -0.26 (0.41), residues: 159 loop : -1.66 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 99 HIS 0.003 0.001 HIS B 519 PHE 0.010 0.001 PHE B 371 TYR 0.010 0.001 TYR C 96 ARG 0.004 0.001 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 73 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.392 Fit side-chains outliers start: 14 outliers final: 13 residues processed: 71 average time/residue: 0.1691 time to fit residues: 15.0439 Evaluate side-chains 71 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER 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 90 VAL 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: 0.9980 chunk 36 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 0.0980 chunk 19 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 0.0870 chunk 39 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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 = 0.3274 r_free = 0.3274 target = 0.088969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.077529 restraints weight = 7460.780| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.54 r_work: 0.2981 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3374 Z= 0.175 Angle : 0.656 13.220 4600 Z= 0.317 Chirality : 0.045 0.151 500 Planarity : 0.004 0.031 594 Dihedral : 4.934 33.721 466 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.39 % Allowed : 23.73 % 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: -1.82 (0.39), residues: 419 helix: -4.74 (0.49), residues: 28 sheet: 0.05 (0.42), residues: 149 loop : -1.62 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS C 104 PHE 0.010 0.001 PHE B 400 TYR 0.009 0.001 TYR B 489 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 74 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.400 Fit side-chains REVERT: B 489 TYR cc_start: 0.5696 (m-10) cc_final: 0.5491 (m-10) outliers start: 12 outliers final: 12 residues processed: 73 average time/residue: 0.1555 time to fit residues: 13.9762 Evaluate side-chains 72 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER 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 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 24 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 28 optimal weight: 0.1980 chunk 31 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3244 r_free = 0.3244 target = 0.087241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.075908 restraints weight = 7486.866| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.52 r_work: 0.2951 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 3374 Z= 0.276 Angle : 0.719 12.019 4600 Z= 0.351 Chirality : 0.047 0.297 500 Planarity : 0.004 0.032 594 Dihedral : 5.135 33.098 466 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 3.95 % Allowed : 23.16 % 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: -1.78 (0.39), residues: 419 helix: -4.73 (0.50), residues: 28 sheet: -0.12 (0.41), residues: 159 loop : -1.50 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 99 HIS 0.003 0.001 HIS C 104 PHE 0.010 0.001 PHE B 400 TYR 0.008 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: 2251.30 seconds wall clock time: 41 minutes 11.98 seconds (2471.98 seconds total)