Mon 24 Dec 07:27:24 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 2i5i-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2i5i-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2i5i-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i5i-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/2i5i-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i5i-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 07:27:28 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/2i5i-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2i5i-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 363 and 0 Target number of residues in the AU: 363 Target solvent content: 0.6507 Checking the provided sequence file Detected sequence length: 263 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 526 Adjusted target solvent content: 0.49 Input MTZ file: 2i5i-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: 146 Cell parameters: 130.530 130.530 85.760 90.000 90.000 120.000 Input sequence file: 2i5i-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 4208 target number of atoms Had to go as low as 0.80 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: 29.446 3.600 Wilson plot Bfac: 78.40 6266 reflections ( 99.19 % complete ) and 0 restraints for refining 4644 atoms. Observations/parameters ratio is 0.34 ------------------------------------------------------ Starting model: R = 0.3494 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2796 (Rfree = 0.000) for 4644 atoms. Found 21 (29 requested) and removed 59 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.52 3.57 Search for helices and strands: 0 residues in 0 chains, 4660 seeds are put forward NCS extension: 0 residues added, 4660 seeds are put forward Round 1: 124 peptides, 29 chains. Longest chain 7 peptides. Score 0.198 Round 2: 180 peptides, 38 chains. Longest chain 11 peptides. Score 0.264 Round 3: 192 peptides, 38 chains. Longest chain 10 peptides. Score 0.303 Round 4: 208 peptides, 40 chains. Longest chain 10 peptides. Score 0.326 Round 5: 191 peptides, 37 chains. Longest chain 8 peptides. Score 0.313 Taking the results from Round 4 Chains 40, Residues 168, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6266 reflections ( 99.19 % complete ) and 9116 restraints for refining 3815 atoms. 8484 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2297 (Rfree = 0.000) for 3815 atoms. Found 7 (24 requested) and removed 21 (12 requested) atoms. Cycle 2: After refmac, R = 0.2085 (Rfree = 0.000) for 3751 atoms. Found 11 (24 requested) and removed 18 (12 requested) atoms. Cycle 3: After refmac, R = 0.2034 (Rfree = 0.000) for 3720 atoms. Found 7 (24 requested) and removed 14 (12 requested) atoms. Cycle 4: After refmac, R = 0.1990 (Rfree = 0.000) for 3706 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. Cycle 5: After refmac, R = 0.1984 (Rfree = 0.000) for 3692 atoms. Found 2 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.48 3.53 Search for helices and strands: 0 residues in 0 chains, 3764 seeds are put forward NCS extension: 0 residues added, 3764 seeds are put forward Round 1: 168 peptides, 36 chains. Longest chain 10 peptides. Score 0.251 Round 2: 214 peptides, 40 chains. Longest chain 11 peptides. Score 0.344 Round 3: 225 peptides, 41 chains. Longest chain 11 peptides. Score 0.365 Round 4: 235 peptides, 41 chains. Longest chain 17 peptides. Score 0.394 Round 5: 227 peptides, 40 chains. Longest chain 10 peptides. Score 0.383 Taking the results from Round 4 Chains 41, Residues 194, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6266 reflections ( 99.19 % complete ) and 8291 restraints for refining 3624 atoms. 7543 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2092 (Rfree = 0.000) for 3624 atoms. Found 12 (23 requested) and removed 30 (11 requested) atoms. Cycle 7: After refmac, R = 0.1993 (Rfree = 0.000) for 3593 atoms. Found 4 (23 requested) and removed 12 (11 requested) atoms. Cycle 8: After refmac, R = 0.1972 (Rfree = 0.000) for 3577 atoms. Found 8 (22 requested) and removed 13 (11 requested) atoms. Cycle 9: After refmac, R = 0.1954 (Rfree = 0.000) for 3569 atoms. Found 4 (22 requested) and removed 14 (11 requested) atoms. Cycle 10: After refmac, R = 0.1940 (Rfree = 0.000) for 3558 atoms. Found 6 (22 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.50 3.55 Search for helices and strands: 0 residues in 0 chains, 3616 seeds are put forward NCS extension: 0 residues added, 3616 seeds are put forward Round 1: 216 peptides, 46 chains. Longest chain 10 peptides. Score 0.273 Round 2: 243 peptides, 45 chains. Longest chain 14 peptides. Score 0.367 Round 3: 250 peptides, 42 chains. Longest chain 13 peptides. Score 0.424 Round 4: 242 peptides, 44 chains. Longest chain 11 peptides. Score 0.377 Round 5: 241 peptides, 40 chains. Longest chain 15 peptides. Score 0.423 Taking the results from Round 3 Chains 42, Residues 208, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6266 reflections ( 99.19 % complete ) and 8068 restraints for refining 3622 atoms. 7278 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2030 (Rfree = 0.000) for 3622 atoms. Found 9 (23 requested) and removed 28 (11 requested) atoms. Cycle 12: After refmac, R = 0.1938 (Rfree = 0.000) for 3591 atoms. Found 0 (23 requested) and removed 15 (11 requested) atoms. Cycle 13: After refmac, R = 0.1929 (Rfree = 0.000) for 3574 atoms. Found 2 (22 requested) and removed 13 (11 requested) atoms. Cycle 14: After refmac, R = 0.1907 (Rfree = 0.000) for 3560 atoms. Found 3 (22 requested) and removed 12 (11 requested) atoms. Cycle 15: After refmac, R = 0.1890 (Rfree = 0.000) for 3549 atoms. Found 1 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.49 3.54 Search for helices and strands: 0 residues in 0 chains, 3615 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3635 seeds are put forward Round 1: 191 peptides, 39 chains. Longest chain 8 peptides. Score 0.286 Round 2: 202 peptides, 36 chains. Longest chain 10 peptides. Score 0.360 Round 3: 217 peptides, 38 chains. Longest chain 11 peptides. Score 0.379 Round 4: 213 peptides, 37 chains. Longest chain 12 peptides. Score 0.380 Round 5: 225 peptides, 40 chains. Longest chain 10 peptides. Score 0.377 Taking the results from Round 4 Chains 37, Residues 176, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6266 reflections ( 99.19 % complete ) and 8606 restraints for refining 3702 atoms. 7939 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1895 (Rfree = 0.000) for 3702 atoms. Found 16 (23 requested) and removed 29 (11 requested) atoms. Cycle 17: After refmac, R = 0.1717 (Rfree = 0.000) for 3666 atoms. Found 7 (23 requested) and removed 14 (11 requested) atoms. Cycle 18: After refmac, R = 0.1661 (Rfree = 0.000) for 3658 atoms. Found 3 (23 requested) and removed 13 (11 requested) atoms. Cycle 19: After refmac, R = 0.1683 (Rfree = 0.000) for 3647 atoms. Found 4 (23 requested) and removed 11 (11 requested) atoms. Cycle 20: After refmac, R = 0.1670 (Rfree = 0.000) for 3638 atoms. Found 2 (23 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.49 3.54 Search for helices and strands: 0 residues in 0 chains, 3686 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3701 seeds are put forward Round 1: 183 peptides, 41 chains. Longest chain 8 peptides. Score 0.232 Round 2: 210 peptides, 42 chains. Longest chain 10 peptides. Score 0.306 Round 3: 205 peptides, 40 chains. Longest chain 8 peptides. Score 0.317 Round 4: 207 peptides, 40 chains. Longest chain 9 peptides. Score 0.323 Round 5: 217 peptides, 39 chains. Longest chain 14 peptides. Score 0.366 Taking the results from Round 5 Chains 39, Residues 178, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6266 reflections ( 99.19 % complete ) and 8909 restraints for refining 3795 atoms. 8236 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1830 (Rfree = 0.000) for 3795 atoms. Found 14 (24 requested) and removed 33 (12 requested) atoms. Cycle 22: After refmac, R = 0.1865 (Rfree = 0.000) for 3764 atoms. Found 24 (24 requested) and removed 24 (12 requested) atoms. Cycle 23: After refmac, R = 0.1522 (Rfree = 0.000) for 3746 atoms. Found 7 (24 requested) and removed 15 (12 requested) atoms. Cycle 24: After refmac, R = 0.1726 (Rfree = 0.000) for 3733 atoms. Found 16 (23 requested) and removed 15 (11 requested) atoms. Cycle 25: After refmac, R = 0.1678 (Rfree = 0.000) for 3726 atoms. Found 13 (23 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.45 3.50 Search for helices and strands: 0 residues in 0 chains, 3784 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 3807 seeds are put forward Round 1: 157 peptides, 35 chains. Longest chain 7 peptides. Score 0.228 Round 2: 192 peptides, 36 chains. Longest chain 9 peptides. Score 0.329 Round 3: 187 peptides, 35 chains. Longest chain 10 peptides. Score 0.327 Round 4: 198 peptides, 39 chains. Longest chain 9 peptides. Score 0.308 Round 5: 197 peptides, 35 chains. Longest chain 11 peptides. Score 0.358 Taking the results from Round 5 Chains 35, Residues 162, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6266 reflections ( 99.19 % complete ) and 8476 restraints for refining 3682 atoms. 7863 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1709 (Rfree = 0.000) for 3682 atoms. Found 23 (23 requested) and removed 29 (11 requested) atoms. Cycle 27: After refmac, R = 0.1629 (Rfree = 0.000) for 3656 atoms. Found 16 (23 requested) and removed 23 (11 requested) atoms. Cycle 28: After refmac, R = 0.1661 (Rfree = 0.000) for 3636 atoms. Found 23 (23 requested) and removed 25 (11 requested) atoms. Cycle 29: After refmac, R = 0.1699 (Rfree = 0.000) for 3624 atoms. Found 18 (23 requested) and removed 29 (11 requested) atoms. Cycle 30: After refmac, R = 0.1559 (Rfree = 0.000) for 3601 atoms. Found 11 (23 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.50 3.55 Search for helices and strands: 0 residues in 0 chains, 3667 seeds are put forward NCS extension: 0 residues added, 3667 seeds are put forward Round 1: 141 peptides, 31 chains. Longest chain 6 peptides. Score 0.230 Round 2: 169 peptides, 31 chains. Longest chain 13 peptides. Score 0.325 Round 3: 164 peptides, 28 chains. Longest chain 17 peptides. Score 0.350 Round 4: 157 peptides, 28 chains. Longest chain 12 peptides. Score 0.328 Round 5: 165 peptides, 27 chains. Longest chain 11 peptides. Score 0.367 Taking the results from Round 5 Chains 27, Residues 138, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6266 reflections ( 99.19 % complete ) and 7962 restraints for refining 3529 atoms. 7437 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1815 (Rfree = 0.000) for 3529 atoms. Found 22 (22 requested) and removed 27 (11 requested) atoms. Cycle 32: After refmac, R = 0.1784 (Rfree = 0.000) for 3520 atoms. Found 20 (22 requested) and removed 18 (11 requested) atoms. Cycle 33: After refmac, R = 0.1663 (Rfree = 0.000) for 3514 atoms. Found 19 (22 requested) and removed 14 (11 requested) atoms. Cycle 34: After refmac, R = 0.1607 (Rfree = 0.000) for 3514 atoms. Found 14 (22 requested) and removed 20 (11 requested) atoms. Cycle 35: After refmac, R = 0.1302 (Rfree = 0.000) for 3506 atoms. Found 5 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.49 3.54 Search for helices and strands: 0 residues in 0 chains, 3551 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3563 seeds are put forward Round 1: 133 peptides, 31 chains. Longest chain 8 peptides. Score 0.201 Round 2: 189 peptides, 37 chains. Longest chain 15 peptides. Score 0.306 Round 3: 199 peptides, 38 chains. Longest chain 18 peptides. Score 0.325 Round 4: 197 peptides, 38 chains. Longest chain 10 peptides. Score 0.318 Round 5: 201 peptides, 38 chains. Longest chain 8 peptides. Score 0.331 Taking the results from Round 5 Chains 38, Residues 163, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6266 reflections ( 99.19 % complete ) and 7947 restraints for refining 3571 atoms. 7333 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1661 (Rfree = 0.000) for 3571 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. Cycle 37: After refmac, R = 0.2077 (Rfree = 0.000) for 3551 atoms. Found 22 (22 requested) and removed 19 (11 requested) atoms. Cycle 38: After refmac, R = 0.1717 (Rfree = 0.000) for 3546 atoms. Found 22 (22 requested) and removed 17 (11 requested) atoms. Cycle 39: After refmac, R = 0.2110 (Rfree = 0.000) for 3543 atoms. Found 22 (22 requested) and removed 26 (11 requested) atoms. Cycle 40: After refmac, R = 0.1541 (Rfree = 0.000) for 3530 atoms. Found 12 (22 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 3.57 Search for helices and strands: 0 residues in 0 chains, 3593 seeds are put forward NCS extension: 0 residues added, 3593 seeds are put forward Round 1: 142 peptides, 33 chains. Longest chain 7 peptides. Score 0.204 Round 2: 153 peptides, 32 chains. Longest chain 9 peptides. Score 0.257 Round 3: 165 peptides, 34 chains. Longest chain 10 peptides. Score 0.270 Round 4: 163 peptides, 32 chains. Longest chain 8 peptides. Score 0.291 Round 5: 164 peptides, 33 chains. Longest chain 9 peptides. Score 0.280 Taking the results from Round 4 Chains 32, Residues 131, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6266 reflections ( 99.19 % complete ) and 8266 restraints for refining 3639 atoms. 7774 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1720 (Rfree = 0.000) for 3639 atoms. Found 17 (23 requested) and removed 23 (11 requested) atoms. Cycle 42: After refmac, R = 0.1629 (Rfree = 0.000) for 3615 atoms. Found 19 (23 requested) and removed 19 (11 requested) atoms. Cycle 43: After refmac, R = 0.1609 (Rfree = 0.000) for 3608 atoms. Found 23 (23 requested) and removed 20 (11 requested) atoms. Cycle 44: After refmac, R = 0.1576 (Rfree = 0.000) for 3606 atoms. Found 23 (23 requested) and removed 16 (11 requested) atoms. Cycle 45: After refmac, R = 0.1203 (Rfree = 0.000) for 3604 atoms. Found 8 (23 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.51 3.56 Search for helices and strands: 0 residues in 0 chains, 3663 seeds are put forward NCS extension: 0 residues added, 3663 seeds are put forward Round 1: 140 peptides, 33 chains. Longest chain 7 peptides. Score 0.197 Round 2: 145 peptides, 29 chains. Longest chain 8 peptides. Score 0.274 Round 3: 141 peptides, 28 chains. Longest chain 8 peptides. Score 0.275 Round 4: 138 peptides, 25 chains. Longest chain 12 peptides. Score 0.309 Round 5: 129 peptides, 25 chains. Longest chain 10 peptides. Score 0.278 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 113, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2i5i-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. Failed to save intermediate PDB 6266 reflections ( 99.19 % complete ) and 8170 restraints for refining 3576 atoms. 7743 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1541 (Rfree = 0.000) for 3576 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.1421 (Rfree = 0.000) for 3555 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.1190 (Rfree = 0.000) for 3533 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1175 (Rfree = 0.000) for 3519 atoms. TimeTaking 41.98