Starting phenix.real_space_refine on Wed Sep 17 03:16:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yw6_39624/09_2025/8yw6_39624.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yw6_39624/09_2025/8yw6_39624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yw6_39624/09_2025/8yw6_39624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yw6_39624/09_2025/8yw6_39624.map" model { file = "/net/cci-nas-00/data/ceres_data/8yw6_39624/09_2025/8yw6_39624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yw6_39624/09_2025/8yw6_39624.cif" } resolution = 3.18 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= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 17 5.16 5 C 1783 2.51 5 N 460 2.21 5 O 484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 2747 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1000 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 118} Chain: "C" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 879 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "A" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 745 Classifications: {'peptide': 93} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 88} Chain: "B" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 123 Unusual residues: {'CDL': 1, 'PC8': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Time building chain proxies: 1.09, per 1000 atoms: 0.40 Number of scatterers: 2747 At special positions: 0 Unit cell: (78.66, 79.23, 91.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 P 3 15.00 O 484 8.00 N 460 7.00 C 1783 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.22 Conformation dependent library (CDL) restraints added in 144.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 614 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 3 sheets defined 61.9% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 28 through 33 Processing helix chain 'B' and resid 40 through 56 removed outlier: 3.708A pdb=" N TRP B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 68 through 86 Processing helix chain 'B' and resid 93 through 125 Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 24 through 34 Proline residue: A 30 - end of helix removed outlier: 3.585A pdb=" N TRP A 34 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 52 through 73 Processing helix chain 'A' and resid 77 through 108 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.321A pdb=" N GLY C 10 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N SER C 114 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL C 12 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.321A pdb=" N GLY C 10 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N SER C 114 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL C 12 " --> pdb=" O SER C 114 " (cutoff:3.500A) 179 hydrogen bonds defined for protein. 489 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: 0.27 Time building geometry restraints manager: 0.29 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: 409 1.30 - 1.43: 777 1.43 - 1.56: 1581 1.56 - 1.68: 19 1.68 - 1.81: 28 Bond restraints: 2814 Sorted by residual: bond pdb=" CB7 CDL B 202 " pdb=" OB8 CDL B 202 " ideal model delta sigma weight residual 1.334 1.435 -0.101 1.10e-02 8.26e+03 8.47e+01 bond pdb=" CA7 CDL B 202 " pdb=" OA8 CDL B 202 " ideal model delta sigma weight residual 1.334 1.433 -0.099 1.10e-02 8.26e+03 8.17e+01 bond pdb=" CB5 CDL B 202 " pdb=" OB6 CDL B 202 " ideal model delta sigma weight residual 1.342 1.440 -0.098 1.50e-02 4.44e+03 4.23e+01 bond pdb=" CA5 CDL B 202 " pdb=" OA6 CDL B 202 " ideal model delta sigma weight residual 1.342 1.438 -0.096 1.50e-02 4.44e+03 4.06e+01 bond pdb=" OB2 CDL B 202 " pdb=" PB2 CDL B 202 " ideal model delta sigma weight residual 1.579 1.669 -0.090 1.50e-02 4.44e+03 3.62e+01 ... (remaining 2809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 3727 3.23 - 6.46: 51 6.46 - 9.69: 7 9.69 - 12.93: 1 12.93 - 16.16: 1 Bond angle restraints: 3787 Sorted by residual: angle pdb=" C51 CDL B 202 " pdb=" CB5 CDL B 202 " pdb=" OB6 CDL B 202 " ideal model delta sigma weight residual 111.33 118.92 -7.59 1.32e+00 5.72e-01 3.30e+01 angle pdb=" O3 PC8 B 201 " pdb=" P1 PC8 B 201 " pdb=" O4 PC8 B 201 " ideal model delta sigma weight residual 93.28 109.44 -16.16 3.00e+00 1.11e-01 2.90e+01 angle pdb=" C31 CDL B 202 " pdb=" CA7 CDL B 202 " pdb=" OA8 CDL B 202 " ideal model delta sigma weight residual 111.64 120.39 -8.75 1.65e+00 3.69e-01 2.83e+01 angle pdb=" C71 CDL B 202 " pdb=" CB7 CDL B 202 " pdb=" OB8 CDL B 202 " ideal model delta sigma weight residual 111.64 120.11 -8.47 1.65e+00 3.69e-01 2.65e+01 angle pdb=" C11 CDL B 202 " pdb=" CA5 CDL B 202 " pdb=" OA6 CDL B 202 " ideal model delta sigma weight residual 111.33 117.31 -5.98 1.32e+00 5.72e-01 2.05e+01 ... (remaining 3782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.93: 1619 32.93 - 65.85: 70 65.85 - 98.78: 3 98.78 - 131.71: 0 131.71 - 164.63: 1 Dihedral angle restraints: 1693 sinusoidal: 734 harmonic: 959 Sorted by residual: dihedral pdb=" O5 PC8 B 201 " pdb=" C7 PC8 B 201 " pdb=" C8 PC8 B 201 " pdb=" O7 PC8 B 201 " ideal model delta sinusoidal sigma weight residual 52.89 -142.48 -164.63 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" CA5 CDL B 202 " pdb=" CA4 CDL B 202 " pdb=" OA6 CDL B 202 " pdb=" CA6 CDL B 202 " ideal model delta sinusoidal sigma weight residual 168.24 75.71 92.53 1 3.00e+01 1.11e-03 1.11e+01 dihedral pdb=" CA TYR C 35 " pdb=" C TYR C 35 " pdb=" N TRP C 36 " pdb=" CA TRP C 36 " ideal model delta harmonic sigma weight residual 180.00 164.68 15.32 0 5.00e+00 4.00e-02 9.39e+00 ... (remaining 1690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 285 0.052 - 0.104: 70 0.104 - 0.155: 26 0.155 - 0.207: 7 0.207 - 0.259: 4 Chirality restraints: 392 Sorted by residual: chirality pdb=" CA THR A 56 " pdb=" N THR A 56 " pdb=" C THR A 56 " pdb=" CB THR A 56 " both_signs ideal model delta sigma weight residual False 2.53 2.78 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA ASN A 77 " pdb=" N ASN A 77 " pdb=" C ASN A 77 " pdb=" CB ASN A 77 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ARG B 62 " pdb=" N ARG B 62 " pdb=" C ARG B 62 " pdb=" CB ARG B 62 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 389 not shown) Planarity restraints: 464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 76 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C ARG A 76 " -0.045 2.00e-02 2.50e+03 pdb=" O ARG A 76 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN A 77 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 24 " -0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO B 25 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 25 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 25 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER C 53 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" C SER C 53 " -0.024 2.00e-02 2.50e+03 pdb=" O SER C 53 " 0.009 2.00e-02 2.50e+03 pdb=" N GLN C 54 " 0.008 2.00e-02 2.50e+03 ... (remaining 461 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 1003 2.90 - 3.40: 2614 3.40 - 3.90: 4765 3.90 - 4.40: 5264 4.40 - 4.90: 8613 Nonbonded interactions: 22259 Sorted by model distance: nonbonded pdb=" OD2 ASP C 73 " pdb=" NZ LYS C 76 " model vdw 2.395 3.120 nonbonded pdb=" O4 PC8 B 201 " pdb=" O7 PC8 B 201 " model vdw 2.468 2.432 nonbonded pdb=" O GLU C 31 " pdb=" OG SER C 53 " model vdw 2.547 3.040 nonbonded pdb=" OD1 ASP B 18 " pdb=" NH2 ARG B 39 " model vdw 2.555 3.120 nonbonded pdb=" C1 PC8 B 201 " pdb=" C3 PC8 B 201 " model vdw 2.609 3.088 ... (remaining 22254 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.770 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 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 : 0.012 0.105 2815 Z= 0.693 Angle : 1.003 16.157 3789 Z= 0.596 Chirality : 0.061 0.259 392 Planarity : 0.004 0.042 464 Dihedral : 16.353 164.632 1076 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 0.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.74 % Allowed : 1.48 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.94 (0.47), residues: 327 helix: 0.65 (0.36), residues: 176 sheet: -0.31 (0.70), residues: 55 loop : 1.64 (0.73), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 97 TYR 0.008 0.000 TYR C 95 PHE 0.001 0.000 PHE A 66 TRP 0.007 0.001 TRP C 102 HIS 0.001 0.000 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.01172 ( 2814) covalent geometry : angle 1.00332 ( 3787) SS BOND : bond 0.01024 ( 1) SS BOND : angle 0.98399 ( 2) hydrogen bonds : bond 0.16961 ( 175) hydrogen bonds : angle 6.83407 ( 489) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.099 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 32 average time/residue: 0.1292 time to fit residues: 4.6680 Evaluate side-chains 23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.0170 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.7618 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.185938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.129149 restraints weight = 2815.240| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.39 r_work: 0.3234 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2815 Z= 0.145 Angle : 0.512 5.602 3789 Z= 0.271 Chirality : 0.043 0.133 392 Planarity : 0.005 0.039 464 Dihedral : 17.144 170.596 476 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.74 % Allowed : 5.19 % Favored : 94.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.69 (0.46), residues: 327 helix: 2.49 (0.38), residues: 173 sheet: 0.02 (0.69), residues: 49 loop : 1.69 (0.65), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 62 TYR 0.015 0.002 TYR C 95 PHE 0.014 0.002 PHE A 69 TRP 0.009 0.001 TRP B 44 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 2814) covalent geometry : angle 0.51206 ( 3787) SS BOND : bond 0.00378 ( 1) SS BOND : angle 0.80654 ( 2) hydrogen bonds : bond 0.03751 ( 175) hydrogen bonds : angle 4.40071 ( 489) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.158 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 22 average time/residue: 0.1056 time to fit residues: 2.7262 Evaluate side-chains 24 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 83 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 10 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.183000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.126653 restraints weight = 2869.656| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.34 r_work: 0.3217 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2815 Z= 0.140 Angle : 0.473 6.031 3789 Z= 0.249 Chirality : 0.041 0.140 392 Planarity : 0.004 0.034 464 Dihedral : 15.240 150.776 476 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.74 % Allowed : 5.56 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.61 (0.47), residues: 327 helix: 2.47 (0.39), residues: 178 sheet: 0.01 (0.68), residues: 51 loop : 1.52 (0.64), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 62 TYR 0.014 0.002 TYR C 95 PHE 0.013 0.001 PHE A 69 TRP 0.008 0.001 TRP B 44 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 2814) covalent geometry : angle 0.47301 ( 3787) SS BOND : bond 0.00356 ( 1) SS BOND : angle 0.63860 ( 2) hydrogen bonds : bond 0.03787 ( 175) hydrogen bonds : angle 4.07848 ( 489) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.099 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 26 average time/residue: 0.0782 time to fit residues: 2.4873 Evaluate side-chains 25 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 0.0050 chunk 13 optimal weight: 9.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.184029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.128538 restraints weight = 2865.895| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.34 r_work: 0.3244 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2815 Z= 0.112 Angle : 0.434 5.290 3789 Z= 0.227 Chirality : 0.040 0.128 392 Planarity : 0.004 0.034 464 Dihedral : 13.811 144.087 476 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.74 % Allowed : 7.04 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.85 (0.47), residues: 327 helix: 2.74 (0.39), residues: 174 sheet: -0.00 (0.66), residues: 51 loop : 1.62 (0.64), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 62 TYR 0.013 0.001 TYR C 95 PHE 0.012 0.001 PHE A 69 TRP 0.008 0.001 TRP B 44 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 2814) covalent geometry : angle 0.43382 ( 3787) SS BOND : bond 0.00449 ( 1) SS BOND : angle 0.81043 ( 2) hydrogen bonds : bond 0.03316 ( 175) hydrogen bonds : angle 3.77803 ( 489) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.152 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 26 average time/residue: 0.0988 time to fit residues: 3.1621 Evaluate side-chains 23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.0770 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 28 optimal weight: 0.0980 chunk 20 optimal weight: 6.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.183260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.128027 restraints weight = 2826.291| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.32 r_work: 0.3238 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2815 Z= 0.112 Angle : 0.432 5.257 3789 Z= 0.226 Chirality : 0.040 0.129 392 Planarity : 0.004 0.033 464 Dihedral : 13.439 140.567 476 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.74 % Allowed : 9.26 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.94 (0.47), residues: 327 helix: 2.77 (0.39), residues: 174 sheet: 0.14 (0.68), residues: 50 loop : 1.65 (0.64), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 62 TYR 0.014 0.001 TYR C 95 PHE 0.012 0.001 PHE A 69 TRP 0.007 0.001 TRP B 44 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 2814) covalent geometry : angle 0.43206 ( 3787) SS BOND : bond 0.00223 ( 1) SS BOND : angle 0.61132 ( 2) hydrogen bonds : bond 0.03307 ( 175) hydrogen bonds : angle 3.68432 ( 489) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.103 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 24 average time/residue: 0.0982 time to fit residues: 2.8284 Evaluate side-chains 21 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 0 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** 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 = 0.3945 r_free = 0.3945 target = 0.182283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.126968 restraints weight = 2840.155| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.34 r_work: 0.3224 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2815 Z= 0.118 Angle : 0.436 5.303 3789 Z= 0.228 Chirality : 0.040 0.129 392 Planarity : 0.004 0.032 464 Dihedral : 12.934 138.018 476 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.90 (0.47), residues: 327 helix: 2.71 (0.39), residues: 174 sheet: 0.24 (0.68), residues: 50 loop : 1.62 (0.64), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 62 TYR 0.013 0.001 TYR C 95 PHE 0.013 0.001 PHE A 69 TRP 0.007 0.001 TRP B 44 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 2814) covalent geometry : angle 0.43563 ( 3787) SS BOND : bond 0.00219 ( 1) SS BOND : angle 0.76645 ( 2) hydrogen bonds : bond 0.03319 ( 175) hydrogen bonds : angle 3.70065 ( 489) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.098 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0976 time to fit residues: 2.7863 Evaluate side-chains 24 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 2 optimal weight: 0.0170 chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** 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 = 0.3948 r_free = 0.3948 target = 0.182590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.128006 restraints weight = 2809.479| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.30 r_work: 0.3238 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2815 Z= 0.111 Angle : 0.426 5.241 3789 Z= 0.222 Chirality : 0.039 0.128 392 Planarity : 0.004 0.033 464 Dihedral : 12.829 136.907 476 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.37 % Allowed : 10.00 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.95 (0.47), residues: 327 helix: 2.74 (0.39), residues: 174 sheet: 0.40 (0.68), residues: 50 loop : 1.57 (0.64), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 62 TYR 0.013 0.001 TYR C 95 PHE 0.012 0.001 PHE A 69 TRP 0.006 0.001 TRP B 50 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 2814) covalent geometry : angle 0.42593 ( 3787) SS BOND : bond 0.00211 ( 1) SS BOND : angle 0.51213 ( 2) hydrogen bonds : bond 0.03231 ( 175) hydrogen bonds : angle 3.63365 ( 489) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.096 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 0.0922 time to fit residues: 2.4078 Evaluate side-chains 21 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.180620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.127557 restraints weight = 2852.366| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.23 r_work: 0.3216 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2815 Z= 0.127 Angle : 0.443 5.351 3789 Z= 0.231 Chirality : 0.040 0.129 392 Planarity : 0.004 0.033 464 Dihedral : 12.783 137.202 476 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.74 % Allowed : 9.63 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.88 (0.46), residues: 327 helix: 2.65 (0.39), residues: 174 sheet: 0.54 (0.69), residues: 50 loop : 1.50 (0.64), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 62 TYR 0.014 0.001 TYR C 95 PHE 0.014 0.001 PHE A 69 TRP 0.007 0.001 TRP B 44 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 2814) covalent geometry : angle 0.44265 ( 3787) SS BOND : bond 0.00232 ( 1) SS BOND : angle 0.51944 ( 2) hydrogen bonds : bond 0.03348 ( 175) hydrogen bonds : angle 3.69533 ( 489) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.063 Fit side-chains REVERT: B 39 ARG cc_start: 0.8549 (mtp85) cc_final: 0.8304 (mtp85) outliers start: 2 outliers final: 1 residues processed: 22 average time/residue: 0.0843 time to fit residues: 2.2419 Evaluate side-chains 23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 11 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.180148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.122068 restraints weight = 2954.489| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.50 r_work: 0.3159 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2815 Z= 0.133 Angle : 0.448 5.524 3789 Z= 0.234 Chirality : 0.040 0.128 392 Planarity : 0.004 0.034 464 Dihedral : 12.795 138.029 476 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.74 % Allowed : 10.00 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.84 (0.47), residues: 327 helix: 2.61 (0.39), residues: 174 sheet: 0.57 (0.71), residues: 50 loop : 1.48 (0.64), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 62 TYR 0.014 0.001 TYR C 95 PHE 0.015 0.001 PHE A 69 TRP 0.008 0.001 TRP B 44 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 2814) covalent geometry : angle 0.44817 ( 3787) SS BOND : bond 0.00221 ( 1) SS BOND : angle 0.59192 ( 2) hydrogen bonds : bond 0.03392 ( 175) hydrogen bonds : angle 3.75100 ( 489) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.061 Fit side-chains REVERT: B 39 ARG cc_start: 0.8579 (mtp85) cc_final: 0.8295 (mtp85) outliers start: 2 outliers final: 0 residues processed: 22 average time/residue: 0.0958 time to fit residues: 2.4338 Evaluate side-chains 21 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 chunk 3 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** 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 = 0.3915 r_free = 0.3915 target = 0.180026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.123243 restraints weight = 2925.216| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.44 r_work: 0.3172 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2815 Z= 0.123 Angle : 0.436 5.377 3789 Z= 0.228 Chirality : 0.040 0.127 392 Planarity : 0.004 0.034 464 Dihedral : 12.662 136.859 476 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.85 (0.47), residues: 327 helix: 2.66 (0.39), residues: 174 sheet: 0.48 (0.71), residues: 50 loop : 1.45 (0.64), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 62 TYR 0.013 0.001 TYR C 95 PHE 0.013 0.001 PHE A 69 TRP 0.006 0.001 TRP B 50 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 2814) covalent geometry : angle 0.43578 ( 3787) SS BOND : bond 0.00196 ( 1) SS BOND : angle 0.61173 ( 2) hydrogen bonds : bond 0.03305 ( 175) hydrogen bonds : angle 3.69409 ( 489) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.106 Fit side-chains REVERT: B 39 ARG cc_start: 0.8572 (mtp85) cc_final: 0.8330 (mtp85) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0965 time to fit residues: 2.4209 Evaluate side-chains 21 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 18 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.179207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.122666 restraints weight = 2835.678| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.38 r_work: 0.3172 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2815 Z= 0.129 Angle : 0.443 5.465 3789 Z= 0.232 Chirality : 0.040 0.128 392 Planarity : 0.004 0.034 464 Dihedral : 12.730 136.927 476 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.83 (0.47), residues: 327 helix: 2.62 (0.39), residues: 174 sheet: 0.55 (0.71), residues: 50 loop : 1.45 (0.64), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 39 TYR 0.013 0.001 TYR C 95 PHE 0.015 0.001 PHE A 69 TRP 0.006 0.001 TRP B 50 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 2814) covalent geometry : angle 0.44277 ( 3787) SS BOND : bond 0.00183 ( 1) SS BOND : angle 0.64134 ( 2) hydrogen bonds : bond 0.03359 ( 175) hydrogen bonds : angle 3.71926 ( 489) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1168.75 seconds wall clock time: 20 minutes 38.62 seconds (1238.62 seconds total)