Mon 24 Dec 00:44:02 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fur-1.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fur-1.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fur-1.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fur-1.8-parrot-mrncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fur-1.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fur-1.8-parrot-mrncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 00:44:07 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fur-1.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fur-1.8-parrot-mrncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 372 and 0 Target number of residues in the AU: 372 Target solvent content: 0.5051 Checking the provided sequence file Detected sequence length: 209 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 418 Adjusted target solvent content: 0.44 Input MTZ file: 2fur-1.8-parrot-mrncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 19 Cell parameters: 61.040 66.690 99.940 90.000 90.000 90.000 Input sequence file: 2fur-1.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3344 target number of atoms Had to go as low as 0.40 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 1 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 55.473 1.798 Wilson plot Bfac: 24.57 38188 reflections ( 99.31 % complete ) and 0 restraints for refining 3713 atoms. Observations/parameters ratio is 2.57 ------------------------------------------------------ Starting model: R = 0.3327 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2860 (Rfree = 0.000) for 3713 atoms. Found 109 (172 requested) and removed 107 (86 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.09 2.26 NCS extension: 0 residues added, 3715 seeds are put forward Round 1: 317 peptides, 26 chains. Longest chain 37 peptides. Score 0.819 Round 2: 338 peptides, 16 chains. Longest chain 69 peptides. Score 0.899 Round 3: 351 peptides, 14 chains. Longest chain 69 peptides. Score 0.917 Round 4: 362 peptides, 10 chains. Longest chain 101 peptides. Score 0.939 Round 5: 366 peptides, 8 chains. Longest chain 85 peptides. Score 0.948 Taking the results from Round 5 Chains 10, Residues 358, Estimated correctness of the model 99.8 % 8 chains (356 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 40 A and 44 A Built loop between residues 127 A and 130 A Built loop between residues 178 A and 181 A Built loop between residues 68 B and 71 B Built loop between residues 145 B and 150 B Built loop between residues 174 B and 181 B 4 chains (377 residues) following loop building 2 chains (375 residues) in sequence following loop building ------------------------------------------------------ 38188 reflections ( 99.31 % complete ) and 3237 restraints for refining 3311 atoms. 223 conditional restraints added. Observations/parameters ratio is 2.88 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2859 (Rfree = 0.000) for 3311 atoms. Found 126 (153 requested) and removed 79 (76 requested) atoms. Cycle 2: After refmac, R = 0.2502 (Rfree = 0.000) for 3355 atoms. Found 104 (152 requested) and removed 45 (77 requested) atoms. Cycle 3: After refmac, R = 0.2333 (Rfree = 0.000) for 3394 atoms. Found 82 (155 requested) and removed 31 (79 requested) atoms. Cycle 4: After refmac, R = 0.2220 (Rfree = 0.000) for 3435 atoms. Found 62 (156 requested) and removed 31 (79 requested) atoms. Cycle 5: After refmac, R = 0.2151 (Rfree = 0.000) for 3461 atoms. Found 64 (157 requested) and removed 31 (80 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.00 2.17 NCS extension: 0 residues added, 3494 seeds are put forward Round 1: 375 peptides, 3 chains. Longest chain 190 peptides. Score 0.967 Round 2: 371 peptides, 5 chains. Longest chain 162 peptides. Score 0.959 Round 3: 380 peptides, 3 chains. Longest chain 191 peptides. Score 0.968 Round 4: 375 peptides, 5 chains. Longest chain 157 peptides. Score 0.961 Round 5: 381 peptides, 4 chains. Longest chain 156 peptides. Score 0.966 Taking the results from Round 3 Chains 3, Residues 377, Estimated correctness of the model 99.9 % 3 chains (377 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 108 B and 111 B 2 chains (379 residues) following loop building 2 chains (379 residues) in sequence following loop building ------------------------------------------------------ 38188 reflections ( 99.31 % complete ) and 3222 restraints for refining 3386 atoms. 175 conditional restraints added. Observations/parameters ratio is 2.82 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2222 (Rfree = 0.000) for 3386 atoms. Found 121 (154 requested) and removed 53 (78 requested) atoms. Cycle 7: After refmac, R = 0.2140 (Rfree = 0.000) for 3451 atoms. Found 56 (157 requested) and removed 49 (80 requested) atoms. Cycle 8: After refmac, R = 0.2053 (Rfree = 0.000) for 3452 atoms. Found 75 (154 requested) and removed 25 (80 requested) atoms. Cycle 9: After refmac, R = 0.2008 (Rfree = 0.000) for 3501 atoms. Found 61 (156 requested) and removed 53 (81 requested) atoms. Cycle 10: After refmac, R = 0.1982 (Rfree = 0.000) for 3507 atoms. Found 78 (152 requested) and removed 40 (81 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.99 2.16 NCS extension: 0 residues added, 3546 seeds are put forward Round 1: 379 peptides, 2 chains. Longest chain 191 peptides. Score 0.971 Round 2: 379 peptides, 2 chains. Longest chain 191 peptides. Score 0.971 Round 3: 373 peptides, 3 chains. Longest chain 188 peptides. Score 0.966 Round 4: 373 peptides, 4 chains. Longest chain 146 peptides. Score 0.963 Round 5: 380 peptides, 4 chains. Longest chain 162 peptides. Score 0.965 Taking the results from Round 2 Chains 3, Residues 377, Estimated correctness of the model 99.9 % 2 chains (374 residues) have been docked in sequence Building loops using Loopy2018 3 chains (377 residues) following loop building 2 chains (374 residues) in sequence following loop building ------------------------------------------------------ 38188 reflections ( 99.31 % complete ) and 3290 restraints for refining 3417 atoms. 274 conditional restraints added. Observations/parameters ratio is 2.79 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2121 (Rfree = 0.000) for 3417 atoms. Found 111 (145 requested) and removed 56 (79 requested) atoms. Cycle 12: After refmac, R = 0.2056 (Rfree = 0.000) for 3472 atoms. Found 74 (145 requested) and removed 53 (80 requested) atoms. Cycle 13: After refmac, R = 0.2016 (Rfree = 0.000) for 3489 atoms. Found 92 (143 requested) and removed 32 (81 requested) atoms. Cycle 14: After refmac, R = 0.1977 (Rfree = 0.000) for 3548 atoms. Found 72 (144 requested) and removed 69 (82 requested) atoms. Cycle 15: After refmac, R = 0.1964 (Rfree = 0.000) for 3549 atoms. Found 100 (141 requested) and removed 64 (82 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.98 2.15 NCS extension: 1 residues added (3 deleted due to clashes), 3587 seeds are put forward Round 1: 378 peptides, 2 chains. Longest chain 191 peptides. Score 0.970 Round 2: 377 peptides, 3 chains. Longest chain 191 peptides. Score 0.967 Round 3: 376 peptides, 5 chains. Longest chain 162 peptides. Score 0.961 Round 4: 372 peptides, 6 chains. Longest chain 152 peptides. Score 0.957 Round 5: 379 peptides, 3 chains. Longest chain 189 peptides. Score 0.968 Taking the results from Round 1 Chains 2, Residues 376, Estimated correctness of the model 99.9 % 2 chains (376 residues) have been docked in sequence Building loops using Loopy2018 2 chains (376 residues) following loop building 2 chains (376 residues) in sequence following loop building ------------------------------------------------------ 38188 reflections ( 99.31 % complete ) and 3263 restraints for refining 3437 atoms. 238 conditional restraints added. Observations/parameters ratio is 2.78 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2075 (Rfree = 0.000) for 3437 atoms. Found 126 (134 requested) and removed 52 (79 requested) atoms. Cycle 17: After refmac, R = 0.2020 (Rfree = 0.000) for 3511 atoms. Found 87 (136 requested) and removed 79 (81 requested) atoms. Cycle 18: After refmac, R = 0.1979 (Rfree = 0.000) for 3517 atoms. Found 98 (134 requested) and removed 60 (81 requested) atoms. Cycle 19: After refmac, R = 0.1967 (Rfree = 0.000) for 3555 atoms. Found 87 (131 requested) and removed 84 (82 requested) atoms. Cycle 20: After refmac, R = 0.1947 (Rfree = 0.000) for 3555 atoms. Found 101 (129 requested) and removed 71 (82 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.99 2.16 NCS extension: 1 residues added (3 deleted due to clashes), 3586 seeds are put forward Round 1: 378 peptides, 3 chains. Longest chain 191 peptides. Score 0.968 Round 2: 372 peptides, 4 chains. Longest chain 191 peptides. Score 0.963 Round 3: 377 peptides, 3 chains. Longest chain 187 peptides. Score 0.967 Round 4: 377 peptides, 4 chains. Longest chain 191 peptides. Score 0.964 Round 5: 376 peptides, 7 chains. Longest chain 155 peptides. Score 0.955 Taking the results from Round 1 Chains 3, Residues 375, Estimated correctness of the model 99.9 % 3 chains (375 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 40 B and 44 B 2 chains (378 residues) following loop building 2 chains (378 residues) in sequence following loop building ------------------------------------------------------ 38188 reflections ( 99.31 % complete ) and 3257 restraints for refining 3441 atoms. 218 conditional restraints added. Observations/parameters ratio is 2.77 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2077 (Rfree = 0.000) for 3441 atoms. Found 114 (121 requested) and removed 63 (79 requested) atoms. Cycle 22: After refmac, R = 0.2014 (Rfree = 0.000) for 3491 atoms. Found 72 (120 requested) and removed 56 (81 requested) atoms. Cycle 23: After refmac, R = 0.1968 (Rfree = 0.000) for 3505 atoms. Found 85 (117 requested) and removed 43 (81 requested) atoms. Cycle 24: After refmac, R = 0.1946 (Rfree = 0.000) for 3544 atoms. Found 66 (115 requested) and removed 61 (82 requested) atoms. Cycle 25: After refmac, R = 0.1917 (Rfree = 0.000) for 3547 atoms. Found 79 (112 requested) and removed 56 (82 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.99 2.16 NCS extension: 79 residues added (112 deleted due to clashes), 3649 seeds are put forward Round 1: 378 peptides, 4 chains. Longest chain 191 peptides. Score 0.965 Round 2: 381 peptides, 2 chains. Longest chain 191 peptides. Score 0.971 Round 3: 378 peptides, 4 chains. Longest chain 171 peptides. Score 0.965 Round 4: 372 peptides, 7 chains. Longest chain 151 peptides. Score 0.953 Round 5: 379 peptides, 3 chains. Longest chain 189 peptides. Score 0.968 Taking the results from Round 2 Chains 2, Residues 379, Estimated correctness of the model 99.9 % 2 chains (379 residues) have been docked in sequence Building loops using Loopy2018 2 chains (379 residues) following loop building 2 chains (379 residues) in sequence following loop building ------------------------------------------------------ 38188 reflections ( 99.31 % complete ) and 3236 restraints for refining 3432 atoms. 184 conditional restraints added. Observations/parameters ratio is 2.78 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2080 (Rfree = 0.000) for 3432 atoms. Found 105 (105 requested) and removed 58 (79 requested) atoms. Cycle 27: After refmac, R = 0.2035 (Rfree = 0.000) for 3477 atoms. Found 84 (103 requested) and removed 50 (80 requested) atoms. Cycle 28: After refmac, R = 0.1962 (Rfree = 0.000) for 3510 atoms. Found 80 (100 requested) and removed 49 (81 requested) atoms. Cycle 29: After refmac, R = 0.1946 (Rfree = 0.000) for 3538 atoms. Found 63 (98 requested) and removed 68 (82 requested) atoms. Cycle 30: After refmac, R = 0.1920 (Rfree = 0.000) for 3533 atoms. Found 88 (95 requested) and removed 51 (81 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.99 2.16 NCS extension: 0 residues added, 3570 seeds are put forward Round 1: 376 peptides, 4 chains. Longest chain 166 peptides. Score 0.964 Round 2: 377 peptides, 5 chains. Longest chain 101 peptides. Score 0.961 Round 3: 377 peptides, 4 chains. Longest chain 166 peptides. Score 0.964 Round 4: 374 peptides, 5 chains. Longest chain 155 peptides. Score 0.960 Round 5: 378 peptides, 3 chains. Longest chain 191 peptides. Score 0.968 Taking the results from Round 5 Chains 3, Residues 375, Estimated correctness of the model 99.9 % 3 chains (375 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 40 B and 44 B 2 chains (378 residues) following loop building 2 chains (378 residues) in sequence following loop building ------------------------------------------------------ 38188 reflections ( 99.31 % complete ) and 3268 restraints for refining 3432 atoms. 229 conditional restraints added. Observations/parameters ratio is 2.78 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2077 (Rfree = 0.000) for 3432 atoms. Found 89 (89 requested) and removed 62 (79 requested) atoms. Cycle 32: After refmac, R = 0.2013 (Rfree = 0.000) for 3458 atoms. Found 86 (86 requested) and removed 48 (80 requested) atoms. Cycle 33: After refmac, R = 0.1957 (Rfree = 0.000) for 3494 atoms. Found 81 (84 requested) and removed 50 (81 requested) atoms. Cycle 34: After refmac, R = 0.1946 (Rfree = 0.000) for 3524 atoms. Found 81 (81 requested) and removed 70 (81 requested) atoms. Cycle 35: After refmac, R = 0.1935 (Rfree = 0.000) for 3535 atoms. Found 82 (82 requested) and removed 62 (82 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.99 2.16 NCS extension: 0 residues added, 3555 seeds are put forward Round 1: 376 peptides, 4 chains. Longest chain 165 peptides. Score 0.964 Round 2: 377 peptides, 3 chains. Longest chain 190 peptides. Score 0.967 Round 3: 376 peptides, 6 chains. Longest chain 138 peptides. Score 0.958 Round 4: 377 peptides, 5 chains. Longest chain 191 peptides. Score 0.961 Round 5: 374 peptides, 7 chains. Longest chain 101 peptides. Score 0.954 Taking the results from Round 2 Chains 3, Residues 374, Estimated correctness of the model 99.9 % 3 chains (374 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 189 B and 193 B 2 chains (377 residues) following loop building 2 chains (377 residues) in sequence following loop building ------------------------------------------------------ 38188 reflections ( 99.31 % complete ) and 3281 restraints for refining 3431 atoms. 254 conditional restraints added. Observations/parameters ratio is 2.78 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2062 (Rfree = 0.000) for 3431 atoms. Found 79 (79 requested) and removed 61 (79 requested) atoms. Cycle 37: After refmac, R = 0.2002 (Rfree = 0.000) for 3448 atoms. Found 73 (80 requested) and removed 36 (80 requested) atoms. Cycle 38: After refmac, R = 0.1936 (Rfree = 0.000) for 3485 atoms. Found 78 (80 requested) and removed 40 (80 requested) atoms. Cycle 39: After refmac, R = 0.1901 (Rfree = 0.000) for 3522 atoms. Found 79 (81 requested) and removed 57 (81 requested) atoms. Cycle 40: After refmac, R = 0.1896 (Rfree = 0.000) for 3543 atoms. Found 80 (82 requested) and removed 59 (82 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.99 2.16 NCS extension: 0 residues added, 3564 seeds are put forward Round 1: 378 peptides, 3 chains. Longest chain 191 peptides. Score 0.968 Round 2: 378 peptides, 4 chains. Longest chain 191 peptides. Score 0.965 Round 3: 377 peptides, 4 chains. Longest chain 191 peptides. Score 0.964 Round 4: 377 peptides, 4 chains. Longest chain 170 peptides. Score 0.964 Round 5: 375 peptides, 6 chains. Longest chain 151 peptides. Score 0.958 Taking the results from Round 1 Chains 3, Residues 375, Estimated correctness of the model 99.9 % 3 chains (375 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 40 B and 44 B 2 chains (378 residues) following loop building 2 chains (378 residues) in sequence following loop building ------------------------------------------------------ 38188 reflections ( 99.31 % complete ) and 3253 restraints for refining 3430 atoms. 214 conditional restraints added. Observations/parameters ratio is 2.78 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2049 (Rfree = 0.000) for 3430 atoms. Found 79 (79 requested) and removed 54 (79 requested) atoms. Cycle 42: After refmac, R = 0.1974 (Rfree = 0.000) for 3455 atoms. Found 77 (80 requested) and removed 30 (80 requested) atoms. Cycle 43: After refmac, R = 0.1926 (Rfree = 0.000) for 3502 atoms. Found 72 (81 requested) and removed 47 (81 requested) atoms. Cycle 44: After refmac, R = 0.1901 (Rfree = 0.000) for 3526 atoms. Found 74 (81 requested) and removed 51 (81 requested) atoms. Cycle 45: After refmac, R = 0.1894 (Rfree = 0.000) for 3547 atoms. Found 82 (82 requested) and removed 67 (82 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.98 2.15 NCS extension: 0 residues added, 3562 seeds are put forward Round 1: 378 peptides, 3 chains. Longest chain 191 peptides. Score 0.968 Round 2: 378 peptides, 3 chains. Longest chain 191 peptides. Score 0.968 Round 3: 376 peptides, 5 chains. Longest chain 146 peptides. Score 0.961 Round 4: 375 peptides, 5 chains. Longest chain 191 peptides. Score 0.961 Round 5: 379 peptides, 3 chains. Longest chain 191 peptides. Score 0.968 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 376, Estimated correctness of the model 99.9 % 3 chains (376 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 179 B and 182 B 2 chains (378 residues) following loop building 2 chains (378 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 38188 reflections ( 99.31 % complete ) and 3039 restraints for refining 2976 atoms. Observations/parameters ratio is 3.21 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2529 (Rfree = 0.000) for 2976 atoms. Found 67 (69 requested) and removed 0 (69 requested) atoms. Cycle 47: After refmac, R = 0.2330 (Rfree = 0.000) for 2976 atoms. Found 44 (70 requested) and removed 0 (70 requested) atoms. Cycle 48: After refmac, R = 0.2193 (Rfree = 0.000) for 2976 atoms. Found 18 (71 requested) and removed 0 (71 requested) atoms. Cycle 49: After refmac, R = 0.2118 (Rfree = 0.000) for 2976 atoms. TimeTaking 54.4