Sun 23 Dec 23:48:56 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 2gb5-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2gb5-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2gb5-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gb5-3.8-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/2gb5-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gb5-3.8-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 ============================================================ Sun 23 Dec 23:49:01 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/2gb5-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2gb5-3.8-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 381 and 0 Target number of residues in the AU: 381 Target solvent content: 0.6498 Checking the provided sequence file Detected sequence length: 269 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 538 Adjusted target solvent content: 0.51 Input MTZ file: 2gb5-3.8-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: 18 Cell parameters: 99.287 103.553 57.270 90.000 90.000 90.000 Input sequence file: 2gb5-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4304 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: 49.644 3.800 Wilson plot Bfac: 77.61 6155 reflections ( 99.32 % complete ) and 0 restraints for refining 4740 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3345 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3407 (Rfree = 0.000) for 4740 atoms. Found 26 (26 requested) and removed 52 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.64 3.59 Search for helices and strands: 0 residues in 0 chains, 4779 seeds are put forward NCS extension: 0 residues added, 4779 seeds are put forward Round 1: 168 peptides, 37 chains. Longest chain 8 peptides. Score 0.235 Round 2: 225 peptides, 40 chains. Longest chain 12 peptides. Score 0.370 Round 3: 252 peptides, 41 chains. Longest chain 28 peptides. Score 0.432 Round 4: 254 peptides, 45 chains. Longest chain 13 peptides. Score 0.391 Round 5: 260 peptides, 41 chains. Longest chain 23 peptides. Score 0.453 Taking the results from Round 5 Chains 41, Residues 219, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6155 reflections ( 99.32 % complete ) and 9112 restraints for refining 3892 atoms. 8240 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3060 (Rfree = 0.000) for 3892 atoms. Found 13 (21 requested) and removed 22 (10 requested) atoms. Cycle 2: After refmac, R = 0.3021 (Rfree = 0.000) for 3792 atoms. Found 13 (21 requested) and removed 18 (10 requested) atoms. Cycle 3: After refmac, R = 0.2997 (Rfree = 0.000) for 3733 atoms. Found 13 (20 requested) and removed 20 (10 requested) atoms. Cycle 4: After refmac, R = 0.2581 (Rfree = 0.000) for 3692 atoms. Found 4 (20 requested) and removed 13 (10 requested) atoms. Cycle 5: After refmac, R = 0.2899 (Rfree = 0.000) for 3664 atoms. Found 14 (20 requested) and removed 23 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.61 3.56 Search for helices and strands: 0 residues in 0 chains, 3741 seeds are put forward NCS extension: 44 residues added (1 deleted due to clashes), 3785 seeds are put forward Round 1: 220 peptides, 48 chains. Longest chain 8 peptides. Score 0.256 Round 2: 263 peptides, 44 chains. Longest chain 13 peptides. Score 0.427 Round 3: 247 peptides, 41 chains. Longest chain 12 peptides. Score 0.419 Round 4: 254 peptides, 42 chains. Longest chain 15 peptides. Score 0.426 Round 5: 263 peptides, 43 chains. Longest chain 13 peptides. Score 0.438 Taking the results from Round 5 Chains 43, Residues 220, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6155 reflections ( 99.32 % complete ) and 8639 restraints for refining 3705 atoms. 7802 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2912 (Rfree = 0.000) for 3705 atoms. Found 20 (20 requested) and removed 31 (10 requested) atoms. Cycle 7: After refmac, R = 0.2914 (Rfree = 0.000) for 3650 atoms. Found 20 (20 requested) and removed 29 (10 requested) atoms. Cycle 8: After refmac, R = 0.2775 (Rfree = 0.000) for 3614 atoms. Found 20 (20 requested) and removed 19 (10 requested) atoms. Cycle 9: After refmac, R = 0.2708 (Rfree = 0.000) for 3586 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 10: After refmac, R = 0.2309 (Rfree = 0.000) for 3575 atoms. Found 2 (19 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.59 3.54 Search for helices and strands: 0 residues in 0 chains, 3642 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 3654 seeds are put forward Round 1: 204 peptides, 40 chains. Longest chain 11 peptides. Score 0.309 Round 2: 226 peptides, 38 chains. Longest chain 13 peptides. Score 0.397 Round 3: 237 peptides, 40 chains. Longest chain 16 peptides. Score 0.403 Round 4: 244 peptides, 40 chains. Longest chain 15 peptides. Score 0.422 Round 5: 257 peptides, 44 chains. Longest chain 13 peptides. Score 0.411 Taking the results from Round 4 Chains 40, Residues 204, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6155 reflections ( 99.32 % complete ) and 8321 restraints for refining 3638 atoms. 7545 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2756 (Rfree = 0.000) for 3638 atoms. Found 20 (20 requested) and removed 36 (10 requested) atoms. Cycle 12: After refmac, R = 0.2479 (Rfree = 0.000) for 3598 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 13: After refmac, R = 0.2346 (Rfree = 0.000) for 3569 atoms. Found 19 (19 requested) and removed 30 (9 requested) atoms. Cycle 14: After refmac, R = 0.2189 (Rfree = 0.000) for 3543 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 15: After refmac, R = 0.2367 (Rfree = 0.000) for 3540 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.54 3.49 Search for helices and strands: 0 residues in 0 chains, 3666 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 3694 seeds are put forward Round 1: 207 peptides, 44 chains. Longest chain 9 peptides. Score 0.267 Round 2: 223 peptides, 40 chains. Longest chain 19 peptides. Score 0.364 Round 3: 243 peptides, 43 chains. Longest chain 10 peptides. Score 0.384 Round 4: 252 peptides, 41 chains. Longest chain 16 peptides. Score 0.432 Round 5: 251 peptides, 43 chains. Longest chain 17 peptides. Score 0.406 Taking the results from Round 4 Chains 42, Residues 211, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6155 reflections ( 99.32 % complete ) and 8823 restraints for refining 3860 atoms. 7989 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2600 (Rfree = 0.000) for 3860 atoms. Found 21 (21 requested) and removed 32 (10 requested) atoms. Cycle 17: After refmac, R = 0.2464 (Rfree = 0.000) for 3817 atoms. Found 21 (21 requested) and removed 23 (10 requested) atoms. Cycle 18: After refmac, R = 0.2050 (Rfree = 0.000) for 3789 atoms. Found 5 (20 requested) and removed 19 (10 requested) atoms. Cycle 19: After refmac, R = 0.1905 (Rfree = 0.000) for 3766 atoms. Found 10 (20 requested) and removed 16 (10 requested) atoms. Cycle 20: After refmac, R = 0.2383 (Rfree = 0.000) for 3758 atoms. Found 20 (20 requested) and removed 19 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.54 3.49 Search for helices and strands: 0 residues in 0 chains, 3849 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 3865 seeds are put forward Round 1: 184 peptides, 38 chains. Longest chain 9 peptides. Score 0.273 Round 2: 211 peptides, 39 chains. Longest chain 10 peptides. Score 0.342 Round 3: 210 peptides, 36 chains. Longest chain 15 peptides. Score 0.377 Round 4: 223 peptides, 37 chains. Longest chain 12 peptides. Score 0.401 Round 5: 231 peptides, 36 chains. Longest chain 13 peptides. Score 0.434 Taking the results from Round 5 Chains 36, Residues 195, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6155 reflections ( 99.32 % complete ) and 9118 restraints for refining 3891 atoms. 8374 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2779 (Rfree = 0.000) for 3891 atoms. Found 21 (21 requested) and removed 29 (10 requested) atoms. Cycle 22: After refmac, R = 0.2557 (Rfree = 0.000) for 3864 atoms. Found 21 (21 requested) and removed 28 (10 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2571 (Rfree = 0.000) for 3833 atoms. Found 21 (21 requested) and removed 21 (10 requested) atoms. Cycle 24: After refmac, R = 0.2427 (Rfree = 0.000) for 3815 atoms. Found 21 (21 requested) and removed 18 (10 requested) atoms. Cycle 25: After refmac, R = 0.2583 (Rfree = 0.000) for 3798 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.58 3.53 Search for helices and strands: 0 residues in 0 chains, 3871 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3889 seeds are put forward Round 1: 174 peptides, 37 chains. Longest chain 9 peptides. Score 0.255 Round 2: 209 peptides, 38 chains. Longest chain 12 peptides. Score 0.349 Round 3: 215 peptides, 38 chains. Longest chain 13 peptides. Score 0.366 Round 4: 200 peptides, 34 chains. Longest chain 16 peptides. Score 0.373 Round 5: 202 peptides, 34 chains. Longest chain 16 peptides. Score 0.379 Taking the results from Round 5 Chains 35, Residues 168, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6155 reflections ( 99.32 % complete ) and 9229 restraints for refining 3893 atoms. 8535 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2715 (Rfree = 0.000) for 3893 atoms. Found 21 (21 requested) and removed 32 (10 requested) atoms. Cycle 27: After refmac, R = 0.2566 (Rfree = 0.000) for 3842 atoms. Found 21 (21 requested) and removed 21 (10 requested) atoms. Cycle 28: After refmac, R = 0.2461 (Rfree = 0.000) for 3821 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. Cycle 29: After refmac, R = 0.2478 (Rfree = 0.000) for 3808 atoms. Found 21 (21 requested) and removed 19 (10 requested) atoms. Cycle 30: After refmac, R = 0.2390 (Rfree = 0.000) for 3794 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.62 3.57 Search for helices and strands: 0 residues in 0 chains, 3865 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3884 seeds are put forward Round 1: 133 peptides, 29 chains. Longest chain 8 peptides. Score 0.229 Round 2: 161 peptides, 32 chains. Longest chain 8 peptides. Score 0.281 Round 3: 181 peptides, 34 chains. Longest chain 10 peptides. Score 0.317 Round 4: 177 peptides, 29 chains. Longest chain 12 peptides. Score 0.370 Round 5: 170 peptides, 28 chains. Longest chain 11 peptides. Score 0.363 Taking the results from Round 4 Chains 29, Residues 148, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6155 reflections ( 99.32 % complete ) and 8689 restraints for refining 3686 atoms. 8126 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2533 (Rfree = 0.000) for 3686 atoms. Found 20 (20 requested) and removed 26 (10 requested) atoms. Cycle 32: After refmac, R = 0.2462 (Rfree = 0.000) for 3661 atoms. Found 20 (20 requested) and removed 19 (10 requested) atoms. Cycle 33: After refmac, R = 0.2261 (Rfree = 0.000) for 3649 atoms. Found 20 (20 requested) and removed 22 (10 requested) atoms. Cycle 34: After refmac, R = 0.2170 (Rfree = 0.000) for 3639 atoms. Found 20 (20 requested) and removed 12 (10 requested) atoms. Cycle 35: After refmac, R = 0.2191 (Rfree = 0.000) for 3640 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.56 3.51 Search for helices and strands: 0 residues in 0 chains, 3723 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3737 seeds are put forward Round 1: 171 peptides, 36 chains. Longest chain 8 peptides. Score 0.258 Round 2: 197 peptides, 39 chains. Longest chain 10 peptides. Score 0.300 Round 3: 198 peptides, 37 chains. Longest chain 12 peptides. Score 0.329 Round 4: 191 peptides, 33 chains. Longest chain 12 peptides. Score 0.360 Round 5: 177 peptides, 32 chains. Longest chain 9 peptides. Score 0.331 Taking the results from Round 4 Chains 33, Residues 158, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6155 reflections ( 99.32 % complete ) and 8909 restraints for refining 3773 atoms. 8310 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2379 (Rfree = 0.000) for 3773 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 37: After refmac, R = 0.2186 (Rfree = 0.000) for 3756 atoms. Found 20 (20 requested) and removed 21 (10 requested) atoms. Cycle 38: After refmac, R = 0.2186 (Rfree = 0.000) for 3743 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 39: After refmac, R = 0.2292 (Rfree = 0.000) for 3737 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 40: After refmac, R = 0.2246 (Rfree = 0.000) for 3734 atoms. Found 20 (20 requested) and removed 23 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.58 3.53 Search for helices and strands: 0 residues in 0 chains, 3817 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3834 seeds are put forward Round 1: 144 peptides, 31 chains. Longest chain 10 peptides. Score 0.238 Round 2: 161 peptides, 33 chains. Longest chain 10 peptides. Score 0.267 Round 3: 167 peptides, 29 chains. Longest chain 12 peptides. Score 0.340 Round 4: 181 peptides, 32 chains. Longest chain 15 peptides. Score 0.343 Round 5: 174 peptides, 32 chains. Longest chain 11 peptides. Score 0.322 Taking the results from Round 4 Chains 32, Residues 149, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 6155 reflections ( 99.32 % complete ) and 8988 restraints for refining 3846 atoms. 8409 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2377 (Rfree = 0.000) for 3846 atoms. Found 21 (21 requested) and removed 29 (10 requested) atoms. Cycle 42: After refmac, R = 0.2347 (Rfree = 0.000) for 3825 atoms. Found 21 (21 requested) and removed 25 (10 requested) atoms. Cycle 43: After refmac, R = 0.2292 (Rfree = 0.000) for 3814 atoms. Found 21 (21 requested) and removed 19 (10 requested) atoms. Cycle 44: After refmac, R = 0.2102 (Rfree = 0.000) for 3813 atoms. Found 16 (20 requested) and removed 17 (10 requested) atoms. Cycle 45: After refmac, R = 0.2000 (Rfree = 0.000) for 3807 atoms. Found 13 (20 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 3.49 Search for helices and strands: 0 residues in 0 chains, 3889 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 3917 seeds are put forward Round 1: 137 peptides, 31 chains. Longest chain 7 peptides. Score 0.214 Round 2: 146 peptides, 29 chains. Longest chain 8 peptides. Score 0.274 Round 3: 158 peptides, 28 chains. Longest chain 12 peptides. Score 0.326 Round 4: 160 peptides, 29 chains. Longest chain 13 peptides. Score 0.319 Round 5: 164 peptides, 29 chains. Longest chain 11 peptides. Score 0.331 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 135, 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 2gb5-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6155 reflections ( 99.32 % complete ) and 9338 restraints for refining 3893 atoms. 8827 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2461 (Rfree = 0.000) for 3893 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2384 (Rfree = 0.000) for 3868 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2209 (Rfree = 0.000) for 3843 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2173 (Rfree = 0.000) for 3821 atoms. TimeTaking 41.17