Starting phenix.real_space_refine on Wed Sep 17 05:15:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zu1_60478/09_2025/8zu1_60478.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zu1_60478/09_2025/8zu1_60478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zu1_60478/09_2025/8zu1_60478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zu1_60478/09_2025/8zu1_60478.map" model { file = "/net/cci-nas-00/data/ceres_data/8zu1_60478/09_2025/8zu1_60478.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zu1_60478/09_2025/8zu1_60478.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 3217 2.51 5 N 818 2.21 5 O 952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5009 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 618, 5009 Classifications: {'peptide': 618} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 583} Time building chain proxies: 1.21, per 1000 atoms: 0.24 Number of scatterers: 5009 At special positions: 0 Unit cell: (68.1472, 76.032, 83.9168, 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 22 16.00 O 952 8.00 N 818 7.00 C 3217 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.38 Conformation dependent library (CDL) restraints added in 155.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1132 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 8 sheets defined 46.4% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 1 through 14 Processing helix chain 'A' and resid 15 through 19 removed outlier: 3.592A pdb=" N GLY A 19 " --> pdb=" O PRO A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 65 Processing helix chain 'A' and resid 67 through 81 Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 108 through 112 Processing helix chain 'A' and resid 128 through 136 Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 195 through 199 removed outlier: 4.366A pdb=" N PHE A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 195 through 199' Processing helix chain 'A' and resid 214 through 236 Processing helix chain 'A' and resid 239 through 253 Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 312 through 321 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.702A pdb=" N GLU A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN A 351 " --> pdb=" O TYR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.816A pdb=" N GLY A 367 " --> pdb=" O SER A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 416 removed outlier: 3.774A pdb=" N ALA A 403 " --> pdb=" O PHE A 399 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A 408 " --> pdb=" O TRP A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 420 No H-bonds generated for 'chain 'A' and resid 418 through 420' Processing helix chain 'A' and resid 421 through 436 Processing helix chain 'A' and resid 479 through 501 Processing helix chain 'A' and resid 505 through 523 removed outlier: 3.727A pdb=" N ARG A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 538 removed outlier: 3.528A pdb=" N TYR A 538 " --> pdb=" O ARG A 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 535 through 538' Processing helix chain 'A' and resid 539 through 544 Processing helix chain 'A' and resid 569 through 578 removed outlier: 3.912A pdb=" N SER A 573 " --> pdb=" O ASP A 570 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LYS A 574 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 591 Processing helix chain 'A' and resid 600 through 616 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 46 removed outlier: 4.573A pdb=" N LEU A 146 " --> pdb=" O ILE A 164 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 102 through 103 removed outlier: 6.502A pdb=" N SER A 114 " --> pdb=" O LYS A 201 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 184 through 185 removed outlier: 3.665A pdb=" N GLN A 208 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR A 287 " --> pdb=" O ASN A 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 361 through 362 Processing sheet with id=AA5, first strand: chain 'A' and resid 437 through 438 removed outlier: 6.566A pdb=" N SER A 475 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU A 450 " --> pdb=" O VAL A 473 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL A 473 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TRP A 452 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL A 471 " --> pdb=" O TRP A 452 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 524 through 525 removed outlier: 3.522A pdb=" N GLY A 528 " --> pdb=" O ASP A 525 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 532 through 533 Processing sheet with id=AA8, first strand: chain 'A' and resid 554 through 555 218 hydrogen bonds defined for protein. 594 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: 0.82 Time building geometry restraints manager: 0.52 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: 1586 1.34 - 1.46: 1182 1.46 - 1.57: 2374 1.57 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 5184 Sorted by residual: bond pdb=" CG GLU A 57 " pdb=" CD GLU A 57 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.14e+00 bond pdb=" CG LEU A 424 " pdb=" CD1 LEU A 424 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.84e+00 bond pdb=" CB ILE A 425 " pdb=" CG2 ILE A 425 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.00e+00 bond pdb=" CB PRO A 113 " pdb=" CG PRO A 113 " ideal model delta sigma weight residual 1.506 1.471 0.035 3.90e-02 6.57e+02 7.90e-01 bond pdb=" C ALA A 38 " pdb=" N PRO A 39 " ideal model delta sigma weight residual 1.334 1.352 -0.018 2.34e-02 1.83e+03 5.92e-01 ... (remaining 5179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 6694 1.13 - 2.26: 286 2.26 - 3.39: 63 3.39 - 4.52: 17 4.52 - 5.65: 5 Bond angle restraints: 7065 Sorted by residual: angle pdb=" CA TYR A 53 " pdb=" CB TYR A 53 " pdb=" CG TYR A 53 " ideal model delta sigma weight residual 113.90 119.12 -5.22 1.80e+00 3.09e-01 8.40e+00 angle pdb=" C LEU A 56 " pdb=" N GLU A 57 " pdb=" CA GLU A 57 " ideal model delta sigma weight residual 121.58 115.93 5.65 1.95e+00 2.63e-01 8.39e+00 angle pdb=" CA TYR A 547 " pdb=" CB TYR A 547 " pdb=" CG TYR A 547 " ideal model delta sigma weight residual 113.90 109.85 4.05 1.80e+00 3.09e-01 5.06e+00 angle pdb=" C VAL A 36 " pdb=" N GLU A 37 " pdb=" CA GLU A 37 " ideal model delta sigma weight residual 123.09 127.14 -4.05 1.94e+00 2.66e-01 4.35e+00 angle pdb=" CA TYR A 242 " pdb=" CB TYR A 242 " pdb=" CG TYR A 242 " ideal model delta sigma weight residual 113.90 110.15 3.75 1.80e+00 3.09e-01 4.33e+00 ... (remaining 7060 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.35: 2647 16.35 - 32.70: 254 32.70 - 49.05: 37 49.05 - 65.40: 11 65.40 - 81.74: 5 Dihedral angle restraints: 2954 sinusoidal: 1158 harmonic: 1796 Sorted by residual: dihedral pdb=" CA TYR A 286 " pdb=" C TYR A 286 " pdb=" N THR A 287 " pdb=" CA THR A 287 " ideal model delta harmonic sigma weight residual 180.00 158.89 21.11 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA TYR A 547 " pdb=" C TYR A 547 " pdb=" N VAL A 548 " pdb=" CA VAL A 548 " ideal model delta harmonic sigma weight residual 180.00 159.98 20.02 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ALA A 38 " pdb=" C ALA A 38 " pdb=" N PRO A 39 " pdb=" CA PRO A 39 " ideal model delta harmonic sigma weight residual 180.00 160.41 19.59 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 2951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 482 0.042 - 0.083: 159 0.083 - 0.124: 43 0.124 - 0.166: 2 0.166 - 0.207: 1 Chirality restraints: 687 Sorted by residual: chirality pdb=" CA GLU A 57 " pdb=" N GLU A 57 " pdb=" C GLU A 57 " pdb=" CB GLU A 57 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB VAL A 546 " pdb=" CA VAL A 546 " pdb=" CG1 VAL A 546 " pdb=" CG2 VAL A 546 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CA ILE A 179 " pdb=" N ILE A 179 " pdb=" C ILE A 179 " pdb=" CB ILE A 179 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 684 not shown) Planarity restraints: 918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 556 " -0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO A 557 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 557 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 557 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 271 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO A 272 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 272 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 272 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 242 " -0.014 2.00e-02 2.50e+03 1.13e-02 2.56e+00 pdb=" CG TYR A 242 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR A 242 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 242 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 242 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 242 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 242 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 242 " -0.000 2.00e-02 2.50e+03 ... (remaining 915 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 71 2.67 - 3.23: 4696 3.23 - 3.79: 8208 3.79 - 4.34: 11548 4.34 - 4.90: 18743 Nonbonded interactions: 43266 Sorted by model distance: nonbonded pdb=" O TYR A 2 " pdb=" ND2 ASN A 611 " model vdw 2.118 3.120 nonbonded pdb=" OH TYR A 28 " pdb=" OD2 ASP A 150 " model vdw 2.179 3.040 nonbonded pdb=" O ARG A 600 " pdb=" NE2 GLN A 604 " model vdw 2.232 3.120 nonbonded pdb=" OE2 GLU A 75 " pdb=" OH TYR A 242 " model vdw 2.249 3.040 nonbonded pdb=" OG SER A 377 " pdb=" O PRO A 456 " model vdw 2.252 3.040 ... (remaining 43261 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.360 Set stop_for_unknowns flag: 0.010 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.540 Find NCS groups from input model: 0.020 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:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5184 Z= 0.155 Angle : 0.572 5.647 7065 Z= 0.305 Chirality : 0.044 0.207 687 Planarity : 0.005 0.045 918 Dihedral : 13.123 81.745 1822 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.33), residues: 616 helix: 1.65 (0.35), residues: 230 sheet: 1.21 (0.96), residues: 27 loop : -0.53 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 472 TYR 0.027 0.002 TYR A 242 PHE 0.010 0.002 PHE A 346 TRP 0.013 0.001 TRP A 602 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 5184) covalent geometry : angle 0.57230 ( 7065) hydrogen bonds : bond 0.16620 ( 218) hydrogen bonds : angle 6.08188 ( 594) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.182 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.6332 time to fit residues: 42.0763 Evaluate side-chains 48 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 0.0470 chunk 48 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.0970 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 488 ASN ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.172747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.150732 restraints weight = 5733.180| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.69 r_work: 0.3635 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5184 Z= 0.109 Angle : 0.508 4.678 7065 Z= 0.269 Chirality : 0.041 0.150 687 Planarity : 0.004 0.040 918 Dihedral : 4.363 20.233 686 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.17 % Allowed : 7.42 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.35), residues: 616 helix: 2.17 (0.34), residues: 227 sheet: 1.48 (0.86), residues: 32 loop : -0.26 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 160 TYR 0.021 0.001 TYR A 242 PHE 0.010 0.001 PHE A 70 TRP 0.010 0.001 TRP A 602 HIS 0.003 0.001 HIS A 129 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 5184) covalent geometry : angle 0.50803 ( 7065) hydrogen bonds : bond 0.04086 ( 218) hydrogen bonds : angle 4.94642 ( 594) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.170 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 55 average time/residue: 0.6644 time to fit residues: 37.8966 Evaluate side-chains 48 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 52 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 54 optimal weight: 0.1980 chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 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 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.172706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.150378 restraints weight = 5749.181| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.74 r_work: 0.3626 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5184 Z= 0.117 Angle : 0.510 9.224 7065 Z= 0.264 Chirality : 0.041 0.132 687 Planarity : 0.004 0.038 918 Dihedral : 4.267 20.203 686 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.37 % Allowed : 9.57 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.35), residues: 616 helix: 2.31 (0.33), residues: 227 sheet: 1.40 (0.87), residues: 32 loop : -0.23 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 160 TYR 0.019 0.001 TYR A 242 PHE 0.009 0.001 PHE A 70 TRP 0.008 0.001 TRP A 602 HIS 0.003 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 5184) covalent geometry : angle 0.51033 ( 7065) hydrogen bonds : bond 0.04052 ( 218) hydrogen bonds : angle 4.72752 ( 594) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.209 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 60 average time/residue: 0.6776 time to fit residues: 42.1999 Evaluate side-chains 50 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 546 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 26 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 34 optimal weight: 0.0980 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 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 = 0.3930 r_free = 0.3930 target = 0.172965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.150927 restraints weight = 5680.907| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.68 r_work: 0.3619 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5184 Z= 0.110 Angle : 0.495 7.654 7065 Z= 0.258 Chirality : 0.041 0.149 687 Planarity : 0.004 0.037 918 Dihedral : 4.190 20.365 686 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.34 % Allowed : 9.77 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.35), residues: 616 helix: 2.39 (0.33), residues: 227 sheet: 1.35 (0.87), residues: 32 loop : -0.27 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 160 TYR 0.024 0.001 TYR A 242 PHE 0.008 0.001 PHE A 70 TRP 0.008 0.001 TRP A 602 HIS 0.003 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 5184) covalent geometry : angle 0.49523 ( 7065) hydrogen bonds : bond 0.03877 ( 218) hydrogen bonds : angle 4.65861 ( 594) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.199 Fit side-chains REVERT: A 104 ASP cc_start: 0.7157 (OUTLIER) cc_final: 0.6872 (t0) outliers start: 12 outliers final: 3 residues processed: 61 average time/residue: 0.6391 time to fit residues: 40.6413 Evaluate side-chains 53 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 546 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.167585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.145045 restraints weight = 5829.631| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.73 r_work: 0.3579 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5184 Z= 0.153 Angle : 0.559 6.972 7065 Z= 0.294 Chirality : 0.042 0.148 687 Planarity : 0.004 0.038 918 Dihedral : 4.478 20.785 686 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.15 % Allowed : 9.77 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.34), residues: 616 helix: 2.19 (0.33), residues: 227 sheet: 1.05 (0.97), residues: 22 loop : -0.40 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 408 TYR 0.023 0.001 TYR A 547 PHE 0.010 0.002 PHE A 346 TRP 0.010 0.001 TRP A 349 HIS 0.005 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 5184) covalent geometry : angle 0.55884 ( 7065) hydrogen bonds : bond 0.04644 ( 218) hydrogen bonds : angle 4.75706 ( 594) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.205 Fit side-chains REVERT: A 104 ASP cc_start: 0.7153 (OUTLIER) cc_final: 0.6811 (t0) REVERT: A 422 LYS cc_start: 0.7404 (pptt) cc_final: 0.6745 (ptpt) REVERT: A 424 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.7079 (tt) outliers start: 11 outliers final: 3 residues processed: 58 average time/residue: 0.7052 time to fit residues: 42.4909 Evaluate side-chains 54 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 546 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 35 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3888 r_free = 0.3888 target = 0.169370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.146965 restraints weight = 5886.240| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.73 r_work: 0.3567 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5184 Z= 0.128 Angle : 0.532 6.341 7065 Z= 0.280 Chirality : 0.041 0.152 687 Planarity : 0.004 0.037 918 Dihedral : 4.389 20.612 686 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.54 % Allowed : 10.94 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.34), residues: 616 helix: 2.24 (0.33), residues: 227 sheet: 1.05 (0.96), residues: 22 loop : -0.38 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 160 TYR 0.024 0.001 TYR A 242 PHE 0.009 0.001 PHE A 346 TRP 0.009 0.001 TRP A 602 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 5184) covalent geometry : angle 0.53189 ( 7065) hydrogen bonds : bond 0.04208 ( 218) hydrogen bonds : angle 4.65552 ( 594) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.196 Fit side-chains REVERT: A 104 ASP cc_start: 0.7126 (OUTLIER) cc_final: 0.6829 (t0) REVERT: A 172 GLN cc_start: 0.7413 (mm110) cc_final: 0.7153 (tp40) outliers start: 13 outliers final: 4 residues processed: 61 average time/residue: 0.7079 time to fit residues: 44.8788 Evaluate side-chains 54 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 546 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 46 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.170866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.148688 restraints weight = 5769.498| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.69 r_work: 0.3588 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5184 Z= 0.119 Angle : 0.526 6.058 7065 Z= 0.276 Chirality : 0.041 0.130 687 Planarity : 0.004 0.036 918 Dihedral : 4.324 20.397 686 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.37 % Allowed : 11.52 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.34), residues: 616 helix: 2.28 (0.33), residues: 227 sheet: 1.11 (0.96), residues: 22 loop : -0.33 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 160 TYR 0.027 0.001 TYR A 242 PHE 0.007 0.001 PHE A 379 TRP 0.009 0.001 TRP A 602 HIS 0.003 0.001 HIS A 181 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 5184) covalent geometry : angle 0.52641 ( 7065) hydrogen bonds : bond 0.03984 ( 218) hydrogen bonds : angle 4.60568 ( 594) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.203 Fit side-chains REVERT: A 104 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6849 (t0) REVERT: A 172 GLN cc_start: 0.7412 (mm110) cc_final: 0.7164 (tp40) REVERT: A 422 LYS cc_start: 0.7293 (pptt) cc_final: 0.6637 (ptpt) outliers start: 7 outliers final: 4 residues processed: 58 average time/residue: 0.7059 time to fit residues: 42.5372 Evaluate side-chains 54 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 546 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 0.4980 chunk 15 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.173474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.151352 restraints weight = 5774.524| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.70 r_work: 0.3642 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5184 Z= 0.110 Angle : 0.513 5.943 7065 Z= 0.270 Chirality : 0.041 0.157 687 Planarity : 0.004 0.035 918 Dihedral : 4.266 20.326 686 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.56 % Allowed : 12.50 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.34), residues: 616 helix: 2.34 (0.33), residues: 227 sheet: 1.16 (0.98), residues: 22 loop : -0.28 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 160 TYR 0.026 0.001 TYR A 242 PHE 0.007 0.001 PHE A 379 TRP 0.010 0.001 TRP A 602 HIS 0.003 0.001 HIS A 181 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 5184) covalent geometry : angle 0.51280 ( 7065) hydrogen bonds : bond 0.03816 ( 218) hydrogen bonds : angle 4.56482 ( 594) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.174 Fit side-chains REVERT: A 172 GLN cc_start: 0.7452 (mm110) cc_final: 0.7205 (tp40) REVERT: A 422 LYS cc_start: 0.7352 (pptt) cc_final: 0.6731 (ptpt) outliers start: 8 outliers final: 4 residues processed: 57 average time/residue: 0.6757 time to fit residues: 40.0450 Evaluate side-chains 53 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 546 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 38 optimal weight: 0.1980 chunk 9 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.171402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.149492 restraints weight = 5792.398| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.66 r_work: 0.3615 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5184 Z= 0.128 Angle : 0.545 9.996 7065 Z= 0.283 Chirality : 0.041 0.149 687 Planarity : 0.004 0.035 918 Dihedral : 4.359 20.125 686 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.56 % Allowed : 12.70 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.34), residues: 616 helix: 2.24 (0.33), residues: 227 sheet: 1.08 (0.98), residues: 22 loop : -0.32 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 160 TYR 0.028 0.001 TYR A 242 PHE 0.009 0.001 PHE A 346 TRP 0.008 0.001 TRP A 602 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 5184) covalent geometry : angle 0.54467 ( 7065) hydrogen bonds : bond 0.04176 ( 218) hydrogen bonds : angle 4.59610 ( 594) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.194 Fit side-chains REVERT: A 172 GLN cc_start: 0.7479 (mm110) cc_final: 0.7222 (tp40) REVERT: A 422 LYS cc_start: 0.7403 (pptt) cc_final: 0.6769 (ptpt) outliers start: 8 outliers final: 5 residues processed: 55 average time/residue: 0.6895 time to fit residues: 39.3894 Evaluate side-chains 54 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 546 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 15 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.172302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.150268 restraints weight = 5779.776| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.67 r_work: 0.3629 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5184 Z= 0.115 Angle : 0.551 9.660 7065 Z= 0.283 Chirality : 0.041 0.145 687 Planarity : 0.004 0.035 918 Dihedral : 4.290 20.558 686 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.17 % Allowed : 13.09 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.35), residues: 616 helix: 2.28 (0.33), residues: 227 sheet: 1.12 (1.00), residues: 22 loop : -0.27 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 160 TYR 0.027 0.001 TYR A 242 PHE 0.007 0.001 PHE A 6 TRP 0.010 0.001 TRP A 602 HIS 0.003 0.001 HIS A 181 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 5184) covalent geometry : angle 0.55127 ( 7065) hydrogen bonds : bond 0.03828 ( 218) hydrogen bonds : angle 4.54026 ( 594) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 172 GLN cc_start: 0.7454 (mm110) cc_final: 0.7185 (tp40) REVERT: A 422 LYS cc_start: 0.7374 (pptt) cc_final: 0.6716 (ptpt) outliers start: 6 outliers final: 4 residues processed: 57 average time/residue: 0.6809 time to fit residues: 40.2155 Evaluate side-chains 52 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 546 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 38 optimal weight: 0.2980 chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.173424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.151438 restraints weight = 5849.206| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.69 r_work: 0.3647 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5184 Z= 0.105 Angle : 0.516 9.644 7065 Z= 0.267 Chirality : 0.040 0.144 687 Planarity : 0.004 0.036 918 Dihedral : 4.192 20.423 686 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.17 % Allowed : 13.48 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.35), residues: 616 helix: 2.41 (0.33), residues: 227 sheet: 1.20 (1.00), residues: 22 loop : -0.26 (0.35), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 160 TYR 0.025 0.001 TYR A 242 PHE 0.007 0.001 PHE A 379 TRP 0.011 0.001 TRP A 231 HIS 0.003 0.001 HIS A 181 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 5184) covalent geometry : angle 0.51619 ( 7065) hydrogen bonds : bond 0.03604 ( 218) hydrogen bonds : angle 4.47464 ( 594) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1944.44 seconds wall clock time: 33 minutes 56.88 seconds (2036.88 seconds total)