Mon 24 Dec 07:31:55 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fno-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2fno-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2fno-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fno-3.6-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2fno-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fno-3.6-parrot-noncs ############### 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 07:32:00 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/noncs/ArpWArp/wArpResults/WorkingDir/2fno-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fno-3.6-parrot-noncs/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 392 and 0 Target number of residues in the AU: 392 Target solvent content: 0.6387 Checking the provided sequence file Detected sequence length: 248 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 496 Adjusted target solvent content: 0.54 Input MTZ file: 2fno-3.6-parrot-noncs.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: 5 Cell parameters: 110.204 50.261 117.660 90.000 115.716 90.000 Input sequence file: 2fno-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 3968 target number of atoms Had to go as low as 0.75 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 3 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: 106.006 3.600 Wilson plot Bfac: 71.28 6884 reflections ( 99.21 % complete ) and 0 restraints for refining 4388 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3352 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3428 (Rfree = 0.000) for 4388 atoms. Found 28 (28 requested) and removed 47 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.53 3.35 Search for helices and strands: 0 residues in 0 chains, 4475 seeds are put forward NCS extension: 0 residues added, 4475 seeds are put forward Round 1: 178 peptides, 38 chains. Longest chain 7 peptides. Score 0.254 Round 2: 220 peptides, 40 chains. Longest chain 13 peptides. Score 0.356 Round 3: 235 peptides, 39 chains. Longest chain 13 peptides. Score 0.410 Round 4: 239 peptides, 36 chains. Longest chain 14 peptides. Score 0.456 Round 5: 229 peptides, 36 chains. Longest chain 15 peptides. Score 0.430 Taking the results from Round 4 Chains 36, Residues 203, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.21 % complete ) and 8198 restraints for refining 3596 atoms. 7397 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2712 (Rfree = 0.000) for 3596 atoms. Found 23 (23 requested) and removed 38 (11 requested) atoms. Cycle 2: After refmac, R = 0.2287 (Rfree = 0.000) for 3535 atoms. Found 10 (22 requested) and removed 23 (11 requested) atoms. Cycle 3: After refmac, R = 0.2172 (Rfree = 0.000) for 3500 atoms. Found 7 (22 requested) and removed 19 (11 requested) atoms. Cycle 4: After refmac, R = 0.2095 (Rfree = 0.000) for 3481 atoms. Found 5 (22 requested) and removed 17 (11 requested) atoms. Cycle 5: After refmac, R = 0.2060 (Rfree = 0.000) for 3463 atoms. Found 5 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 3.28 Search for helices and strands: 0 residues in 0 chains, 3590 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3603 seeds are put forward Round 1: 220 peptides, 43 chains. Longest chain 10 peptides. Score 0.319 Round 2: 251 peptides, 40 chains. Longest chain 15 peptides. Score 0.441 Round 3: 238 peptides, 34 chains. Longest chain 19 peptides. Score 0.476 Round 4: 261 peptides, 39 chains. Longest chain 15 peptides. Score 0.478 Round 5: 276 peptides, 43 chains. Longest chain 15 peptides. Score 0.472 Taking the results from Round 4 Chains 39, Residues 222, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.21 % complete ) and 8082 restraints for refining 3553 atoms. 7209 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2577 (Rfree = 0.000) for 3553 atoms. Found 22 (22 requested) and removed 52 (11 requested) atoms. Cycle 7: After refmac, R = 0.2335 (Rfree = 0.000) for 3493 atoms. Found 21 (22 requested) and removed 32 (11 requested) atoms. Cycle 8: After refmac, R = 0.2595 (Rfree = 0.000) for 3462 atoms. Found 22 (22 requested) and removed 52 (11 requested) atoms. Cycle 9: After refmac, R = 0.2533 (Rfree = 0.000) for 3417 atoms. Found 22 (22 requested) and removed 32 (11 requested) atoms. Cycle 10: After refmac, R = 0.2522 (Rfree = 0.000) for 3393 atoms. Found 21 (21 requested) and removed 34 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.68 3.49 Search for helices and strands: 0 residues in 0 chains, 3530 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3545 seeds are put forward Round 1: 204 peptides, 38 chains. Longest chain 13 peptides. Score 0.335 Round 2: 249 peptides, 39 chains. Longest chain 17 peptides. Score 0.448 Round 3: 258 peptides, 39 chains. Longest chain 17 peptides. Score 0.471 Round 4: 241 peptides, 33 chains. Longest chain 18 peptides. Score 0.495 Round 5: 253 peptides, 37 chains. Longest chain 18 peptides. Score 0.480 Taking the results from Round 4 Chains 34, Residues 208, Estimated correctness of the model 0.0 % 4 chains (31 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.21 % complete ) and 8057 restraints for refining 3597 atoms. 7155 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2893 (Rfree = 0.000) for 3597 atoms. Found 23 (23 requested) and removed 48 (11 requested) atoms. Cycle 12: After refmac, R = 0.2370 (Rfree = 0.000) for 3556 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. Cycle 13: After refmac, R = 0.2171 (Rfree = 0.000) for 3543 atoms. Found 22 (22 requested) and removed 17 (11 requested) atoms. Cycle 14: After refmac, R = 0.2091 (Rfree = 0.000) for 3540 atoms. Found 13 (22 requested) and removed 14 (11 requested) atoms. Cycle 15: After refmac, R = 0.2028 (Rfree = 0.000) for 3533 atoms. Found 14 (22 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 3.25 Search for helices and strands: 0 residues in 0 chains, 3668 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3684 seeds are put forward Round 1: 200 peptides, 40 chains. Longest chain 10 peptides. Score 0.297 Round 2: 249 peptides, 43 chains. Longest chain 13 peptides. Score 0.401 Round 3: 234 peptides, 37 chains. Longest chain 11 peptides. Score 0.431 Round 4: 251 peptides, 42 chains. Longest chain 12 peptides. Score 0.418 Round 5: 253 peptides, 38 chains. Longest chain 17 peptides. Score 0.469 Taking the results from Round 5 Chains 38, Residues 215, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.21 % complete ) and 8355 restraints for refining 3596 atoms. 7514 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2370 (Rfree = 0.000) for 3596 atoms. Found 20 (23 requested) and removed 16 (11 requested) atoms. Cycle 17: After refmac, R = 0.2166 (Rfree = 0.000) for 3586 atoms. Found 12 (23 requested) and removed 21 (11 requested) atoms. Cycle 18: After refmac, R = 0.2104 (Rfree = 0.000) for 3564 atoms. Found 14 (22 requested) and removed 15 (11 requested) atoms. Cycle 19: After refmac, R = 0.2298 (Rfree = 0.000) for 3555 atoms. Found 22 (22 requested) and removed 15 (11 requested) atoms. Cycle 20: After refmac, R = 0.2487 (Rfree = 0.000) for 3553 atoms. Found 22 (22 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 3.28 Search for helices and strands: 0 residues in 0 chains, 3708 seeds are put forward NCS extension: 37 residues added (0 deleted due to clashes), 3745 seeds are put forward Round 1: 214 peptides, 42 chains. Longest chain 9 peptides. Score 0.314 Round 2: 262 peptides, 41 chains. Longest chain 15 peptides. Score 0.459 Round 3: 257 peptides, 42 chains. Longest chain 17 peptides. Score 0.434 Round 4: 246 peptides, 38 chains. Longest chain 16 peptides. Score 0.451 Round 5: 249 peptides, 39 chains. Longest chain 14 peptides. Score 0.448 Taking the results from Round 2 Chains 42, Residues 221, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.21 % complete ) and 8046 restraints for refining 3596 atoms. 7124 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2230 (Rfree = 0.000) for 3596 atoms. Found 17 (23 requested) and removed 15 (11 requested) atoms. Cycle 22: After refmac, R = 0.2138 (Rfree = 0.000) for 3579 atoms. Found 15 (23 requested) and removed 16 (11 requested) atoms. Cycle 23: After refmac, R = 0.2333 (Rfree = 0.000) for 3562 atoms. Found 22 (22 requested) and removed 15 (11 requested) atoms. Cycle 24: After refmac, R = 0.2116 (Rfree = 0.000) for 3561 atoms. Found 16 (22 requested) and removed 13 (11 requested) atoms. Cycle 25: After refmac, R = 0.2163 (Rfree = 0.000) for 3553 atoms. Found 22 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.45 3.27 Search for helices and strands: 0 residues in 0 chains, 3721 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3735 seeds are put forward Round 1: 208 peptides, 42 chains. Longest chain 12 peptides. Score 0.296 Round 2: 245 peptides, 43 chains. Longest chain 12 peptides. Score 0.390 Round 3: 254 peptides, 44 chains. Longest chain 12 peptides. Score 0.403 Round 4: 265 peptides, 41 chains. Longest chain 14 peptides. Score 0.466 Round 5: 241 peptides, 41 chains. Longest chain 12 peptides. Score 0.403 Taking the results from Round 4 Chains 41, Residues 224, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.21 % complete ) and 8410 restraints for refining 3597 atoms. 7540 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2245 (Rfree = 0.000) for 3597 atoms. Found 23 (23 requested) and removed 19 (11 requested) atoms. Cycle 27: After refmac, R = 0.2265 (Rfree = 0.000) for 3590 atoms. Found 23 (23 requested) and removed 13 (11 requested) atoms. Cycle 28: After refmac, R = 0.2033 (Rfree = 0.000) for 3596 atoms. Found 16 (23 requested) and removed 15 (11 requested) atoms. Cycle 29: After refmac, R = 0.2108 (Rfree = 0.000) for 3594 atoms. Found 19 (23 requested) and removed 14 (11 requested) atoms. Cycle 30: After refmac, R = 0.1964 (Rfree = 0.000) for 3594 atoms. Found 9 (23 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.50 3.32 Search for helices and strands: 0 residues in 0 chains, 3757 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 3774 seeds are put forward Round 1: 195 peptides, 38 chains. Longest chain 8 peptides. Score 0.308 Round 2: 227 peptides, 40 chains. Longest chain 12 peptides. Score 0.376 Round 3: 236 peptides, 38 chains. Longest chain 13 peptides. Score 0.425 Round 4: 232 peptides, 37 chains. Longest chain 16 peptides. Score 0.426 Round 5: 233 peptides, 36 chains. Longest chain 15 peptides. Score 0.440 Taking the results from Round 5 Chains 36, Residues 197, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.21 % complete ) and 8604 restraints for refining 3597 atoms. 7852 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2347 (Rfree = 0.000) for 3597 atoms. Found 23 (23 requested) and removed 13 (11 requested) atoms. Cycle 32: After refmac, R = 0.2281 (Rfree = 0.000) for 3591 atoms. Found 23 (23 requested) and removed 17 (11 requested) atoms. Cycle 33: After refmac, R = 0.2131 (Rfree = 0.000) for 3591 atoms. Found 23 (23 requested) and removed 16 (11 requested) atoms. Cycle 34: After refmac, R = 0.1951 (Rfree = 0.000) for 3590 atoms. Found 6 (23 requested) and removed 14 (11 requested) atoms. Cycle 35: After refmac, R = 0.1899 (Rfree = 0.000) for 3578 atoms. Found 11 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.49 3.31 Search for helices and strands: 0 residues in 0 chains, 3722 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3739 seeds are put forward Round 1: 180 peptides, 38 chains. Longest chain 7 peptides. Score 0.261 Round 2: 197 peptides, 37 chains. Longest chain 12 peptides. Score 0.327 Round 3: 197 peptides, 34 chains. Longest chain 11 peptides. Score 0.365 Round 4: 201 peptides, 32 chains. Longest chain 12 peptides. Score 0.401 Round 5: 201 peptides, 33 chains. Longest chain 14 peptides. Score 0.389 Taking the results from Round 4 Chains 32, Residues 169, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.21 % complete ) and 8737 restraints for refining 3597 atoms. 8093 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2305 (Rfree = 0.000) for 3597 atoms. Found 23 (23 requested) and removed 17 (11 requested) atoms. Cycle 37: After refmac, R = 0.2029 (Rfree = 0.000) for 3591 atoms. Found 10 (23 requested) and removed 16 (11 requested) atoms. Cycle 38: After refmac, R = 0.2007 (Rfree = 0.000) for 3582 atoms. Found 18 (22 requested) and removed 13 (11 requested) atoms. Cycle 39: After refmac, R = 0.1889 (Rfree = 0.000) for 3583 atoms. Found 5 (22 requested) and removed 11 (11 requested) atoms. Cycle 40: After refmac, R = 0.1830 (Rfree = 0.000) for 3575 atoms. Found 1 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 3.30 Search for helices and strands: 0 residues in 0 chains, 3710 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3729 seeds are put forward Round 1: 172 peptides, 36 chains. Longest chain 9 peptides. Score 0.262 Round 2: 210 peptides, 34 chains. Longest chain 11 peptides. Score 0.402 Round 3: 222 peptides, 35 chains. Longest chain 13 peptides. Score 0.423 Round 4: 222 peptides, 34 chains. Longest chain 13 peptides. Score 0.435 Round 5: 209 peptides, 32 chains. Longest chain 13 peptides. Score 0.423 Taking the results from Round 4 Chains 36, Residues 188, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.21 % complete ) and 8328 restraints for refining 3597 atoms. 7542 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2232 (Rfree = 0.000) for 3597 atoms. Found 21 (23 requested) and removed 15 (11 requested) atoms. Cycle 42: After refmac, R = 0.2017 (Rfree = 0.000) for 3597 atoms. Found 15 (23 requested) and removed 12 (11 requested) atoms. Cycle 43: After refmac, R = 0.1929 (Rfree = 0.000) for 3592 atoms. Found 12 (23 requested) and removed 11 (11 requested) atoms. Cycle 44: After refmac, R = 0.1884 (Rfree = 0.000) for 3587 atoms. Found 6 (23 requested) and removed 11 (11 requested) atoms. Cycle 45: After refmac, R = 0.1902 (Rfree = 0.000) for 3575 atoms. Found 13 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.49 3.31 Search for helices and strands: 0 residues in 0 chains, 3698 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3712 seeds are put forward Round 1: 166 peptides, 33 chains. Longest chain 10 peptides. Score 0.283 Round 2: 195 peptides, 34 chains. Longest chain 11 peptides. Score 0.359 Round 3: 215 peptides, 34 chains. Longest chain 14 peptides. Score 0.416 Round 4: 200 peptides, 33 chains. Longest chain 12 peptides. Score 0.386 Round 5: 199 peptides, 37 chains. Longest chain 11 peptides. Score 0.333 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 181, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2fno-3_warpNtrace.pdb as input Building loops using Loopy2018 34 chains (181 residues) following loop building 2 chains (6 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6884 reflections ( 99.21 % complete ) and 8497 restraints for refining 3597 atoms. 7791 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2132 (Rfree = 0.000) for 3597 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2007 (Rfree = 0.000) for 3572 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.1908 (Rfree = 0.000) for 3554 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1892 (Rfree = 0.000) for 3540 atoms. TimeTaking 41.67