Starting phenix.real_space_refine on Wed Sep 17 06:13:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jig_61505/09_2025/9jig_61505.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jig_61505/09_2025/9jig_61505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jig_61505/09_2025/9jig_61505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jig_61505/09_2025/9jig_61505.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jig_61505/09_2025/9jig_61505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jig_61505/09_2025/9jig_61505.map" } resolution = 2.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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 3646 2.51 5 N 984 2.21 5 O 1140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s 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: 5784 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1128 Classifications: {'peptide': 148} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 139} Chain: "H" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 961 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 120} Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 803 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "B" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1128 Classifications: {'peptide': 148} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 139} Chain: "E" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 961 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 120} Chain: "F" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 803 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 102} Time building chain proxies: 1.67, per 1000 atoms: 0.29 Number of scatterers: 5784 At special positions: 0 Unit cell: (109.2, 66.95, 83.85, 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 1140 8.00 N 984 7.00 C 3646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 89 " distance=2.03 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: 0.50 Conformation dependent library (CDL) restraints added in 253.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1376 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 13 sheets defined 4.3% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 515 through 518 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.577A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.860A pdb=" N GLU L 84 " --> pdb=" O THR L 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 518 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.848A pdb=" N GLU F 84 " --> pdb=" O THR F 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 464 through 465 Processing sheet with id=AA2, first strand: chain 'A' and resid 507 through 510 removed outlier: 4.179A pdb=" N THR A 497 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A 477 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL A 593 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N PHE A 547 " --> pdb=" O GLY A 556 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 492 through 495 removed outlier: 4.976A pdb=" N SER A 582 " --> pdb=" O GLN A 568 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N GLN A 568 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 58 through 60 current: chain 'H' and resid 111 through 114 Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 12 current: chain 'L' and resid 46 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 46 through 49 current: chain 'L' and resid 98 through 101 No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'L' and resid 17 through 23 Processing sheet with id=AA8, first strand: chain 'B' and resid 464 through 465 Processing sheet with id=AA9, first strand: chain 'B' and resid 470 through 481 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 492 through 495 current: chain 'B' and resid 507 through 510 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 507 through 510 current: chain 'B' and resid 534 through 549 removed outlier: 4.712A pdb=" N PHE B 547 " --> pdb=" O GLY B 556 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 555 through 556 current: chain 'B' and resid 579 through 582 Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 11 through 12 current: chain 'E' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 58 through 60 current: chain 'E' and resid 111 through 114 Processing sheet with id=AB3, first strand: chain 'F' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 9 through 12 current: chain 'F' and resid 46 through 49 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 46 through 49 current: chain 'F' and resid 98 through 101 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 17 through 23 118 hydrogen bonds defined for protein. 282 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: 0.84 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 935 1.30 - 1.43: 1665 1.43 - 1.56: 3300 1.56 - 1.69: 0 1.69 - 1.82: 18 Bond restraints: 5918 Sorted by residual: bond pdb=" C VAL B 464 " pdb=" O VAL B 464 " ideal model delta sigma weight residual 1.236 1.176 0.060 1.19e-02 7.06e+03 2.56e+01 bond pdb=" N PRO B 575 " pdb=" CD PRO B 575 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.70e+01 bond pdb=" N PRO A 575 " pdb=" CD PRO A 575 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.69e+01 bond pdb=" C ALA A 574 " pdb=" N PRO A 575 " ideal model delta sigma weight residual 1.332 1.387 -0.055 1.34e-02 5.57e+03 1.68e+01 bond pdb=" C ARG B 466 " pdb=" O ARG B 466 " ideal model delta sigma weight residual 1.234 1.187 0.048 1.28e-02 6.10e+03 1.38e+01 ... (remaining 5913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 7950 2.39 - 4.78: 103 4.78 - 7.16: 19 7.16 - 9.55: 6 9.55 - 11.94: 2 Bond angle restraints: 8080 Sorted by residual: angle pdb=" C ALA B 574 " pdb=" N PRO B 575 " pdb=" CA PRO B 575 " ideal model delta sigma weight residual 119.84 128.02 -8.18 1.25e+00 6.40e-01 4.28e+01 angle pdb=" N PHE B 462 " pdb=" CA PHE B 462 " pdb=" CB PHE B 462 " ideal model delta sigma weight residual 110.12 117.88 -7.76 1.47e+00 4.63e-01 2.79e+01 angle pdb=" CB ARG B 460 " pdb=" CG ARG B 460 " pdb=" CD ARG B 460 " ideal model delta sigma weight residual 111.30 99.36 11.94 2.30e+00 1.89e-01 2.70e+01 angle pdb=" CA ALA A 574 " pdb=" C ALA A 574 " pdb=" N PRO A 575 " ideal model delta sigma weight residual 117.60 123.57 -5.97 1.18e+00 7.18e-01 2.56e+01 angle pdb=" N PRO B 461 " pdb=" CA PRO B 461 " pdb=" CB PRO B 461 " ideal model delta sigma weight residual 103.32 99.46 3.86 8.40e-01 1.42e+00 2.11e+01 ... (remaining 8075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 3099 17.42 - 34.84: 241 34.84 - 52.27: 82 52.27 - 69.69: 16 69.69 - 87.11: 8 Dihedral angle restraints: 3446 sinusoidal: 1268 harmonic: 2178 Sorted by residual: dihedral pdb=" CD ARG B 466 " pdb=" NE ARG B 466 " pdb=" CZ ARG B 466 " pdb=" NH1 ARG B 466 " ideal model delta sinusoidal sigma weight residual 0.00 33.55 -33.55 1 1.00e+01 1.00e-02 1.60e+01 dihedral pdb=" CA GLU H 89 " pdb=" C GLU H 89 " pdb=" N ASP H 90 " pdb=" CA ASP H 90 " ideal model delta harmonic sigma weight residual 180.00 163.79 16.21 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA VAL H 104 " pdb=" C VAL H 104 " pdb=" N GLU H 105 " pdb=" CA GLU H 105 " ideal model delta harmonic sigma weight residual 180.00 -163.79 -16.21 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 3443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 789 0.067 - 0.134: 121 0.134 - 0.201: 4 0.201 - 0.268: 2 0.268 - 0.335: 2 Chirality restraints: 918 Sorted by residual: chirality pdb=" CA PRO A 461 " pdb=" N PRO A 461 " pdb=" C PRO A 461 " pdb=" CB PRO A 461 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CA PRO B 461 " pdb=" N PRO B 461 " pdb=" C PRO B 461 " pdb=" CB PRO B 461 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA ALA B 467 " pdb=" N ALA B 467 " pdb=" C ALA B 467 " pdb=" CB ALA B 467 " both_signs ideal model delta sigma weight residual False 2.48 2.25 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 915 not shown) Planarity restraints: 1034 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 466 " -0.606 9.50e-02 1.11e+02 2.71e-01 4.50e+01 pdb=" NE ARG B 466 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG B 466 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 466 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 466 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 460 " -0.302 9.50e-02 1.11e+02 1.35e-01 1.13e+01 pdb=" NE ARG A 460 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 460 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 460 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 460 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 578 " -0.251 9.50e-02 1.11e+02 1.12e-01 7.74e+00 pdb=" NE ARG A 578 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 578 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 578 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 578 " -0.009 2.00e-02 2.50e+03 ... (remaining 1031 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 509 2.74 - 3.28: 5506 3.28 - 3.82: 10090 3.82 - 4.36: 12452 4.36 - 4.90: 20467 Nonbonded interactions: 49024 Sorted by model distance: nonbonded pdb=" OG1 THR A 585 " pdb=" O VAL H 104 " model vdw 2.205 3.040 nonbonded pdb=" OG1 THR B 585 " pdb=" O VAL E 104 " model vdw 2.285 3.040 nonbonded pdb=" N VAL L 34 " pdb=" OD1 ASN L 52 " model vdw 2.321 3.120 nonbonded pdb=" OE1 GLN F 38 " pdb=" NZ LYS F 46 " model vdw 2.327 3.120 nonbonded pdb=" N VAL F 34 " pdb=" OD1 ASN F 52 " model vdw 2.341 3.120 ... (remaining 49019 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'L' } 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: 6.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.420 Find NCS groups from input model: 0.080 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:8.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 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 : 0.005 0.075 5920 Z= 0.288 Angle : 0.720 11.941 8084 Z= 0.409 Chirality : 0.049 0.335 918 Planarity : 0.012 0.271 1034 Dihedral : 15.100 87.109 2064 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.32 % Allowed : 14.87 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.02 (0.31), residues: 752 helix: None (None), residues: 0 sheet: 1.05 (0.30), residues: 330 loop : -0.94 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 460 TYR 0.025 0.002 TYR H 60 PHE 0.014 0.003 PHE H 68 TRP 0.009 0.002 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00505 ( 5918) covalent geometry : angle 0.72008 ( 8080) SS BOND : bond 0.00206 ( 2) SS BOND : angle 1.15587 ( 4) hydrogen bonds : bond 0.21727 ( 118) hydrogen bonds : angle 7.98854 ( 282) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 159 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: H 6 GLU cc_start: 0.8333 (mp0) cc_final: 0.8023 (mp0) REVERT: E 6 GLU cc_start: 0.8401 (mp0) cc_final: 0.8054 (mp0) REVERT: E 13 GLN cc_start: 0.7500 (mt0) cc_final: 0.7269 (mt0) outliers start: 2 outliers final: 0 residues processed: 161 average time/residue: 0.3958 time to fit residues: 67.5745 Evaluate side-chains 143 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 0.0670 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 GLN H 39 GLN H 77 ASN B 490 ASN B 502 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.128993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.120802 restraints weight = 6728.495| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.18 r_work: 0.3517 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5920 Z= 0.212 Angle : 0.632 7.709 8084 Z= 0.333 Chirality : 0.046 0.142 918 Planarity : 0.005 0.034 1034 Dihedral : 5.972 52.683 840 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.48 % Allowed : 19.78 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.01 (0.31), residues: 752 helix: None (None), residues: 0 sheet: 0.99 (0.29), residues: 328 loop : -0.83 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 460 TYR 0.016 0.002 TYR B 561 PHE 0.018 0.003 PHE B 500 TRP 0.012 0.002 TRP E 47 HIS 0.009 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 5918) covalent geometry : angle 0.63066 ( 8080) SS BOND : bond 0.00297 ( 2) SS BOND : angle 1.78834 ( 4) hydrogen bonds : bond 0.04502 ( 118) hydrogen bonds : angle 5.75839 ( 282) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: H 113 TYR cc_start: 0.7561 (t80) cc_final: 0.7087 (t80) REVERT: E 6 GLU cc_start: 0.8282 (mp0) cc_final: 0.8067 (mp0) REVERT: E 13 GLN cc_start: 0.7758 (mt0) cc_final: 0.7459 (mt0) outliers start: 22 outliers final: 16 residues processed: 164 average time/residue: 0.3974 time to fit residues: 69.3058 Evaluate side-chains 170 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 54 LYS Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 100 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 48 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 GLN H 116 GLN B 502 ASN B 568 GLN E 74 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.127853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.119867 restraints weight = 6683.255| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.14 r_work: 0.3507 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 5920 Z= 0.264 Angle : 0.673 7.670 8084 Z= 0.354 Chirality : 0.048 0.170 918 Planarity : 0.005 0.040 1034 Dihedral : 6.367 57.530 840 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.91 % Allowed : 19.78 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.13 (0.31), residues: 752 helix: None (None), residues: 0 sheet: 0.83 (0.29), residues: 328 loop : -0.86 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 19 TYR 0.017 0.002 TYR B 561 PHE 0.020 0.003 PHE B 500 TRP 0.014 0.002 TRP E 47 HIS 0.015 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00610 ( 5918) covalent geometry : angle 0.67152 ( 8080) SS BOND : bond 0.00335 ( 2) SS BOND : angle 1.95581 ( 4) hydrogen bonds : bond 0.04539 ( 118) hydrogen bonds : angle 5.70013 ( 282) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 0.243 Fit side-chains REVERT: H 113 TYR cc_start: 0.7547 (t80) cc_final: 0.7038 (t80) REVERT: E 6 GLU cc_start: 0.8270 (mp0) cc_final: 0.7986 (mp0) REVERT: E 13 GLN cc_start: 0.7818 (mt0) cc_final: 0.7526 (mt0) outliers start: 31 outliers final: 21 residues processed: 161 average time/residue: 0.4437 time to fit residues: 75.7394 Evaluate side-chains 173 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 17 MET Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 54 LYS Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 100 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 0.0050 chunk 49 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 GLN B 502 ASN B 568 GLN E 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.129740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.121493 restraints weight = 6670.753| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.18 r_work: 0.3529 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5920 Z= 0.185 Angle : 0.590 6.377 8084 Z= 0.312 Chirality : 0.045 0.143 918 Planarity : 0.004 0.037 1034 Dihedral : 6.119 59.175 840 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.43 % Allowed : 19.78 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.12 (0.31), residues: 752 helix: None (None), residues: 0 sheet: 0.79 (0.29), residues: 328 loop : -0.80 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 19 TYR 0.012 0.002 TYR B 561 PHE 0.018 0.003 PHE B 500 TRP 0.013 0.002 TRP E 47 HIS 0.010 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 5918) covalent geometry : angle 0.58906 ( 8080) SS BOND : bond 0.00285 ( 2) SS BOND : angle 1.51250 ( 4) hydrogen bonds : bond 0.03893 ( 118) hydrogen bonds : angle 5.37757 ( 282) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7900 (tmt170) cc_final: 0.7676 (ttt180) REVERT: H 113 TYR cc_start: 0.7533 (t80) cc_final: 0.7011 (t80) REVERT: E 6 GLU cc_start: 0.8263 (mp0) cc_final: 0.7963 (mp0) REVERT: E 13 GLN cc_start: 0.7888 (mt0) cc_final: 0.7596 (mt0) outliers start: 28 outliers final: 15 residues processed: 171 average time/residue: 0.4311 time to fit residues: 77.9362 Evaluate side-chains 172 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain L residue 17 MET Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 100 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 12 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 51 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 GLN A 531 GLN L 38 GLN B 502 ASN B 568 GLN E 74 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.129173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.121006 restraints weight = 6792.223| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.17 r_work: 0.3523 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5920 Z= 0.206 Angle : 0.611 6.511 8084 Z= 0.323 Chirality : 0.045 0.143 918 Planarity : 0.004 0.039 1034 Dihedral : 6.212 60.931 840 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.80 % Allowed : 20.73 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.14 (0.31), residues: 752 helix: None (None), residues: 0 sheet: 0.75 (0.29), residues: 328 loop : -0.79 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 19 TYR 0.013 0.002 TYR B 561 PHE 0.019 0.003 PHE A 547 TRP 0.014 0.002 TRP E 47 HIS 0.013 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 5918) covalent geometry : angle 0.61043 ( 8080) SS BOND : bond 0.00284 ( 2) SS BOND : angle 1.57730 ( 4) hydrogen bonds : bond 0.03965 ( 118) hydrogen bonds : angle 5.32403 ( 282) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: H 113 TYR cc_start: 0.7535 (t80) cc_final: 0.7007 (t80) REVERT: E 6 GLU cc_start: 0.8253 (mp0) cc_final: 0.7956 (mp0) REVERT: E 13 GLN cc_start: 0.7847 (mt0) cc_final: 0.7576 (mt0) outliers start: 24 outliers final: 17 residues processed: 165 average time/residue: 0.4244 time to fit residues: 74.1784 Evaluate side-chains 172 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain L residue 17 MET Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 70 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 4 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 0.4980 chunk 73 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 GLN B 502 ASN B 568 GLN ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.128414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.120268 restraints weight = 6746.139| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.17 r_work: 0.3512 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 5920 Z= 0.248 Angle : 0.647 7.041 8084 Z= 0.342 Chirality : 0.047 0.148 918 Planarity : 0.005 0.040 1034 Dihedral : 6.429 62.299 840 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.96 % Allowed : 20.41 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.18 (0.31), residues: 752 helix: None (None), residues: 0 sheet: 0.70 (0.29), residues: 328 loop : -0.80 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 19 TYR 0.015 0.002 TYR B 561 PHE 0.021 0.003 PHE A 547 TRP 0.014 0.002 TRP E 47 HIS 0.014 0.003 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00574 ( 5918) covalent geometry : angle 0.64611 ( 8080) SS BOND : bond 0.00301 ( 2) SS BOND : angle 1.73289 ( 4) hydrogen bonds : bond 0.04175 ( 118) hydrogen bonds : angle 5.43717 ( 282) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 529 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7796 (tt) REVERT: H 60 TYR cc_start: 0.7237 (m-10) cc_final: 0.6974 (m-10) REVERT: H 113 TYR cc_start: 0.7534 (t80) cc_final: 0.7001 (t80) REVERT: E 6 GLU cc_start: 0.8265 (mp0) cc_final: 0.7974 (mp0) REVERT: E 13 GLN cc_start: 0.7856 (mt0) cc_final: 0.7582 (mt0) outliers start: 25 outliers final: 21 residues processed: 161 average time/residue: 0.4261 time to fit residues: 72.6455 Evaluate side-chains 175 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 17 MET Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 100 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 28 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 45 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 GLN L 38 GLN B 502 ASN B 568 GLN ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.129218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.121037 restraints weight = 6706.429| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.17 r_work: 0.3521 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5920 Z= 0.205 Angle : 0.608 6.471 8084 Z= 0.322 Chirality : 0.045 0.144 918 Planarity : 0.004 0.040 1034 Dihedral : 6.274 61.686 840 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.11 % Allowed : 20.57 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.14 (0.31), residues: 752 helix: None (None), residues: 0 sheet: 0.70 (0.29), residues: 328 loop : -0.73 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 19 TYR 0.012 0.002 TYR B 561 PHE 0.020 0.003 PHE A 547 TRP 0.014 0.002 TRP E 47 HIS 0.011 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 5918) covalent geometry : angle 0.60683 ( 8080) SS BOND : bond 0.00275 ( 2) SS BOND : angle 1.53849 ( 4) hydrogen bonds : bond 0.03882 ( 118) hydrogen bonds : angle 5.33579 ( 282) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 529 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7792 (tt) REVERT: H 60 TYR cc_start: 0.7216 (m-10) cc_final: 0.6963 (m-10) REVERT: H 113 TYR cc_start: 0.7520 (t80) cc_final: 0.6985 (t80) REVERT: E 6 GLU cc_start: 0.8245 (mp0) cc_final: 0.7953 (mp0) REVERT: E 13 GLN cc_start: 0.7786 (mt0) cc_final: 0.7534 (mt0) outliers start: 26 outliers final: 21 residues processed: 162 average time/residue: 0.4284 time to fit residues: 73.5242 Evaluate side-chains 174 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 17 MET Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 100 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 72 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 0.0470 chunk 51 optimal weight: 3.9990 chunk 53 optimal weight: 0.0970 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 GLN A 531 GLN L 31 ASN L 38 GLN B 568 GLN ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.130016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.121801 restraints weight = 6709.642| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.18 r_work: 0.3539 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5920 Z= 0.166 Angle : 0.571 5.995 8084 Z= 0.302 Chirality : 0.044 0.143 918 Planarity : 0.004 0.040 1034 Dihedral : 6.017 59.419 840 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.11 % Allowed : 20.89 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.07 (0.31), residues: 752 helix: None (None), residues: 0 sheet: 0.73 (0.29), residues: 328 loop : -0.69 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 19 TYR 0.014 0.002 TYR E 113 PHE 0.018 0.003 PHE A 547 TRP 0.013 0.002 TRP E 47 HIS 0.009 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 5918) covalent geometry : angle 0.57010 ( 8080) SS BOND : bond 0.00240 ( 2) SS BOND : angle 1.30053 ( 4) hydrogen bonds : bond 0.03622 ( 118) hydrogen bonds : angle 5.19798 ( 282) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: H 113 TYR cc_start: 0.7508 (t80) cc_final: 0.6970 (t80) REVERT: E 6 GLU cc_start: 0.8239 (mp0) cc_final: 0.7933 (mp0) REVERT: E 13 GLN cc_start: 0.7787 (mt0) cc_final: 0.7540 (mt0) outliers start: 26 outliers final: 20 residues processed: 159 average time/residue: 0.4114 time to fit residues: 69.4295 Evaluate side-chains 169 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 17 MET Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 100 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 38 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 32 optimal weight: 0.0670 chunk 26 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.0980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 GLN L 31 ASN ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 GLN E 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.130784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.122492 restraints weight = 6724.600| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.20 r_work: 0.3545 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5920 Z= 0.153 Angle : 0.564 5.896 8084 Z= 0.297 Chirality : 0.044 0.149 918 Planarity : 0.004 0.040 1034 Dihedral : 5.884 57.509 840 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.80 % Allowed : 22.63 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.08 (0.31), residues: 752 helix: None (None), residues: 0 sheet: 0.73 (0.29), residues: 318 loop : -0.66 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 19 TYR 0.014 0.001 TYR E 113 PHE 0.018 0.003 PHE A 547 TRP 0.012 0.002 TRP E 47 HIS 0.008 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 5918) covalent geometry : angle 0.56341 ( 8080) SS BOND : bond 0.00247 ( 2) SS BOND : angle 1.25577 ( 4) hydrogen bonds : bond 0.03526 ( 118) hydrogen bonds : angle 5.18319 ( 282) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: H 113 TYR cc_start: 0.7505 (t80) cc_final: 0.6971 (t80) REVERT: E 6 GLU cc_start: 0.8228 (mp0) cc_final: 0.7926 (mp0) REVERT: E 13 GLN cc_start: 0.7706 (mt0) cc_final: 0.7490 (mt0) outliers start: 24 outliers final: 20 residues processed: 160 average time/residue: 0.4067 time to fit residues: 69.0173 Evaluate side-chains 169 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 17 MET Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 549 GLU Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 0.0000 chunk 63 optimal weight: 0.0020 chunk 8 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 GLN L 31 ASN L 38 GLN B 568 GLN E 74 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.130431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.122122 restraints weight = 6757.539| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.20 r_work: 0.3539 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5920 Z= 0.169 Angle : 0.582 6.682 8084 Z= 0.306 Chirality : 0.044 0.154 918 Planarity : 0.004 0.041 1034 Dihedral : 5.941 57.127 840 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.32 % Allowed : 23.26 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.08 (0.31), residues: 752 helix: None (None), residues: 0 sheet: 0.73 (0.29), residues: 318 loop : -0.65 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 19 TYR 0.013 0.002 TYR E 113 PHE 0.018 0.003 PHE A 547 TRP 0.013 0.002 TRP E 47 HIS 0.009 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 5918) covalent geometry : angle 0.58122 ( 8080) SS BOND : bond 0.00235 ( 2) SS BOND : angle 1.29186 ( 4) hydrogen bonds : bond 0.03620 ( 118) hydrogen bonds : angle 5.21264 ( 282) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: H 113 TYR cc_start: 0.7513 (t80) cc_final: 0.6974 (t80) REVERT: E 6 GLU cc_start: 0.8243 (mp0) cc_final: 0.7935 (mp0) REVERT: E 13 GLN cc_start: 0.7710 (mt0) cc_final: 0.7494 (mt0) outliers start: 21 outliers final: 21 residues processed: 155 average time/residue: 0.4222 time to fit residues: 69.4816 Evaluate side-chains 168 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 17 MET Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 549 GLU Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 63 optimal weight: 0.0070 chunk 34 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 5 optimal weight: 0.0980 chunk 64 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 62 optimal weight: 0.4980 overall best weight: 0.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 GLN A 531 GLN L 31 ASN L 38 GLN B 568 GLN ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.131992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.123589 restraints weight = 6710.080| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.22 r_work: 0.3559 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5920 Z= 0.124 Angle : 0.534 6.289 8084 Z= 0.281 Chirality : 0.043 0.150 918 Planarity : 0.004 0.040 1034 Dihedral : 5.544 52.488 840 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.22 % Allowed : 24.37 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.01 (0.31), residues: 752 helix: None (None), residues: 0 sheet: 0.76 (0.29), residues: 318 loop : -0.59 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 19 TYR 0.014 0.001 TYR E 113 PHE 0.017 0.002 PHE A 547 TRP 0.011 0.001 TRP E 47 HIS 0.006 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 5918) covalent geometry : angle 0.53346 ( 8080) SS BOND : bond 0.00207 ( 2) SS BOND : angle 1.02133 ( 4) hydrogen bonds : bond 0.03268 ( 118) hydrogen bonds : angle 4.99651 ( 282) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2567.70 seconds wall clock time: 44 minutes 34.25 seconds (2674.25 seconds total)