Mon 24 Dec 01:09:04 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 2pnk-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pnk-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pnk-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pnk-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/2pnk-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pnk-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 ============================================================ Mon 24 Dec 01:09:09 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/2pnk-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pnk-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 4485 and 0 Target number of residues in the AU: 4485 Target solvent content: 0.6566 Target number of residues exceeds 1700, conditional restraints are disabled Checking the provided sequence file Detected sequence length: 428 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 12 Adjusted target number of residues: 5136 Adjusted target solvent content: 0.61 Input MTZ file: 2pnk-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: 5 Cell parameters: 273.720 158.560 181.240 90.000 116.029 90.000 Input sequence file: 2pnk-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 41088 target number of atoms Had to go as low as 1.00 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. 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: 162.857 3.800 Wilson plot Bfac: 82.54 63786 reflections ( 92.90 % complete ) and 0 restraints for refining 45268 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3184 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2768 (Rfree = 0.000) for 45268 atoms. Found 248 (248 requested) and removed 248 (124 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.65 3.14 Search for helices and strands: 0 residues in 0 chains, 46344 seeds are put forward NCS extension: 0 residues added, 46344 seeds are put forward Round 1: 2542 peptides, 441 chains. Longest chain 17 peptides. Score 0.373 Round 2: 3088 peptides, 426 chains. Longest chain 24 peptides. Score 0.507 Round 3: 3187 peptides, 398 chains. Longest chain 28 peptides. Score 0.550 Round 4: 3259 peptides, 396 chains. Longest chain 26 peptides. Score 0.565 Round 5: 3273 peptides, 388 chains. Longest chain 37 peptides. Score 0.575 Taking the results from Round 5 Chains 396, Residues 2885, Estimated correctness of the model 0.0 % 11 chains (129 residues) have been docked in sequence ------------------------------------------------------ 63786 reflections ( 92.90 % complete ) and 11661 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2084 (Rfree = 0.000) for 37165 atoms. Found 204 (204 requested) and removed 203 (102 requested) atoms. Cycle 2: After refmac, R = 0.1918 (Rfree = 0.000) for 37166 atoms. Found 171 (204 requested) and removed 164 (102 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.1854 (Rfree = 0.000) for 37173 atoms. Found 204 (204 requested) and removed 189 (102 requested) atoms. Cycle 4: After refmac, R = 0.1768 (Rfree = 0.000) for 37188 atoms. Found 204 (204 requested) and removed 191 (102 requested) atoms. Cycle 5: After refmac, R = 0.1384 (Rfree = 0.000) for 37201 atoms. Found 33 (204 requested) and removed 151 (102 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.63 3.13 Search for helices and strands: 0 residues in 0 chains, 38558 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 38571 seeds are put forward Round 1: 2871 peptides, 443 chains. Longest chain 26 peptides. Score 0.445 Round 2: 3218 peptides, 403 chains. Longest chain 33 peptides. Score 0.552 Round 3: 3207 peptides, 380 chains. Longest chain 33 peptides. Score 0.569 Round 4: 3295 peptides, 379 chains. Longest chain 33 peptides. Score 0.586 Round 5: 3279 peptides, 385 chains. Longest chain 28 peptides. Score 0.578 Taking the results from Round 4 Chains 386, Residues 2916, Estimated correctness of the model 0.0 % 10 chains (127 residues) have been docked in sequence ------------------------------------------------------ 63786 reflections ( 92.90 % complete ) and 11791 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1908 (Rfree = 0.000) for 37165 atoms. Found 182 (204 requested) and removed 160 (102 requested) atoms. Cycle 7: After refmac, R = 0.1781 (Rfree = 0.000) for 37187 atoms. Found 174 (204 requested) and removed 162 (102 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.1725 (Rfree = 0.000) for 37199 atoms. Found 195 (204 requested) and removed 191 (102 requested) atoms. Cycle 9: After refmac, R = 0.1305 (Rfree = 0.000) for 37203 atoms. Found 33 (204 requested) and removed 136 (102 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1237 (Rfree = 0.000) for 37100 atoms. Found 16 (204 requested) and removed 144 (102 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.63 3.13 Search for helices and strands: 0 residues in 0 chains, 38391 seeds are put forward NCS extension: 0 residues added, 38391 seeds are put forward Round 1: 2842 peptides, 425 chains. Longest chain 25 peptides. Score 0.456 Round 2: 3137 peptides, 396 chains. Longest chain 29 peptides. Score 0.543 Round 3: 3189 peptides, 398 chains. Longest chain 35 peptides. Score 0.551 Round 4: 3255 peptides, 393 chains. Longest chain 30 peptides. Score 0.567 Round 5: 3292 peptides, 383 chains. Longest chain 34 peptides. Score 0.582 Taking the results from Round 5 Chains 396, Residues 2909, Estimated correctness of the model 0.0 % 19 chains (219 residues) have been docked in sequence ------------------------------------------------------ 63786 reflections ( 92.90 % complete ) and 12135 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1854 (Rfree = 0.000) for 37165 atoms. Found 201 (204 requested) and removed 151 (102 requested) atoms. Cycle 12: After refmac, R = 0.1767 (Rfree = 0.000) for 37215 atoms. Found 204 (204 requested) and removed 155 (102 requested) atoms. Cycle 13: After refmac, R = 0.1716 (Rfree = 0.000) for 37264 atoms. Found 204 (204 requested) and removed 176 (102 requested) atoms. Cycle 14: After refmac, R = 0.1309 (Rfree = 0.000) for 37292 atoms. Found 20 (205 requested) and removed 151 (102 requested) atoms. Cycle 15: After refmac, R = 0.1238 (Rfree = 0.000) for 37161 atoms. Found 14 (204 requested) and removed 131 (102 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.64 3.14 Search for helices and strands: 0 residues in 0 chains, 38425 seeds are put forward NCS extension: 0 residues added, 38425 seeds are put forward Round 1: 2802 peptides, 435 chains. Longest chain 26 peptides. Score 0.438 Round 2: 3140 peptides, 406 chains. Longest chain 25 peptides. Score 0.535 Round 3: 3212 peptides, 398 chains. Longest chain 35 peptides. Score 0.555 Round 4: 3159 peptides, 391 chains. Longest chain 27 peptides. Score 0.551 Round 5: 3150 peptides, 374 chains. Longest chain 38 peptides. Score 0.564 Taking the results from Round 5 Chains 394, Residues 2776, Estimated correctness of the model 0.0 % 20 chains (234 residues) have been docked in sequence ------------------------------------------------------ 63786 reflections ( 92.90 % complete ) and 11728 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1890 (Rfree = 0.000) for 37165 atoms. Found 202 (204 requested) and removed 154 (102 requested) atoms. Cycle 17: After refmac, R = 0.1769 (Rfree = 0.000) for 37213 atoms. Found 201 (204 requested) and removed 137 (102 requested) atoms. Cycle 18: After refmac, R = 0.1685 (Rfree = 0.000) for 37277 atoms. Found 183 (205 requested) and removed 173 (102 requested) atoms. Cycle 19: After refmac, R = 0.1647 (Rfree = 0.000) for 37287 atoms. Found 205 (205 requested) and removed 153 (102 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1585 (Rfree = 0.000) for 37339 atoms. Found 193 (205 requested) and removed 169 (102 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.62 3.12 Search for helices and strands: 0 residues in 0 chains, 38775 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 38790 seeds are put forward Round 1: 2619 peptides, 437 chains. Longest chain 19 peptides. Score 0.395 Round 2: 2900 peptides, 401 chains. Longest chain 26 peptides. Score 0.491 Round 3: 3024 peptides, 408 chains. Longest chain 24 peptides. Score 0.510 Round 4: 3001 peptides, 395 chains. Longest chain 28 peptides. Score 0.517 Round 5: 2974 peptides, 391 chains. Longest chain 24 peptides. Score 0.515 Taking the results from Round 4 Chains 398, Residues 2606, Estimated correctness of the model 0.0 % 15 chains (122 residues) have been docked in sequence ------------------------------------------------------ 63786 reflections ( 92.90 % complete ) and 10513 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1865 (Rfree = 0.000) for 37165 atoms. Found 204 (204 requested) and removed 159 (102 requested) atoms. Cycle 22: After refmac, R = 0.1799 (Rfree = 0.000) for 37210 atoms. Found 204 (204 requested) and removed 159 (102 requested) atoms. Cycle 23: After refmac, R = 0.1725 (Rfree = 0.000) for 37255 atoms. Found 204 (204 requested) and removed 142 (102 requested) atoms. Cycle 24: After refmac, R = 0.1692 (Rfree = 0.000) for 37317 atoms. Found 205 (205 requested) and removed 170 (102 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1281 (Rfree = 0.000) for 37352 atoms. Found 16 (205 requested) and removed 136 (102 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.63 3.13 Search for helices and strands: 0 residues in 0 chains, 38614 seeds are put forward NCS extension: 0 residues added, 38614 seeds are put forward Round 1: 2550 peptides, 437 chains. Longest chain 20 peptides. Score 0.379 Round 2: 2898 peptides, 412 chains. Longest chain 22 peptides. Score 0.481 Round 3: 2899 peptides, 411 chains. Longest chain 23 peptides. Score 0.482 Round 4: 2873 peptides, 401 chains. Longest chain 25 peptides. Score 0.486 Round 5: 2904 peptides, 410 chains. Longest chain 24 peptides. Score 0.484 Taking the results from Round 4 Chains 409, Residues 2472, Estimated correctness of the model 0.0 % 10 chains (86 residues) have been docked in sequence ------------------------------------------------------ 63786 reflections ( 92.90 % complete ) and 9804 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1796 (Rfree = 0.000) for 37165 atoms. Found 204 (204 requested) and removed 145 (102 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1744 (Rfree = 0.000) for 37224 atoms. Found 204 (204 requested) and removed 155 (102 requested) atoms. Cycle 28: After refmac, R = 0.1290 (Rfree = 0.000) for 37273 atoms. Found 14 (204 requested) and removed 137 (102 requested) atoms. Cycle 29: After refmac, R = 0.1211 (Rfree = 0.000) for 37150 atoms. Found 19 (204 requested) and removed 129 (102 requested) atoms. Cycle 30: After refmac, R = 0.1193 (Rfree = 0.000) for 37040 atoms. Found 17 (203 requested) and removed 120 (101 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.64 3.14 Search for helices and strands: 0 residues in 0 chains, 38216 seeds are put forward NCS extension: 0 residues added, 38216 seeds are put forward Round 1: 2431 peptides, 451 chains. Longest chain 18 peptides. Score 0.335 Round 2: 2740 peptides, 417 chains. Longest chain 18 peptides. Score 0.442 Round 3: 2791 peptides, 406 chains. Longest chain 34 peptides. Score 0.464 Round 4: 2840 peptides, 408 chains. Longest chain 22 peptides. Score 0.472 Round 5: 2808 peptides, 406 chains. Longest chain 23 peptides. Score 0.467 Taking the results from Round 4 Chains 412, Residues 2432, Estimated correctness of the model 0.0 % 8 chains (94 residues) have been docked in sequence ------------------------------------------------------ 63786 reflections ( 92.90 % complete ) and 9707 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1825 (Rfree = 0.000) for 37165 atoms. Found 204 (204 requested) and removed 142 (102 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.1724 (Rfree = 0.000) for 37227 atoms. Found 204 (204 requested) and removed 154 (102 requested) atoms. Cycle 33: After refmac, R = 0.1274 (Rfree = 0.000) for 37277 atoms. Found 26 (205 requested) and removed 141 (102 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1186 (Rfree = 0.000) for 37162 atoms. Found 23 (204 requested) and removed 129 (102 requested) atoms. Cycle 35: After refmac, R = 0.1160 (Rfree = 0.000) for 37056 atoms. Found 21 (203 requested) and removed 129 (101 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.64 3.14 Search for helices and strands: 0 residues in 0 chains, 38217 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 38234 seeds are put forward Round 1: 2338 peptides, 433 chains. Longest chain 19 peptides. Score 0.331 Round 2: 2704 peptides, 425 chains. Longest chain 21 peptides. Score 0.426 Round 3: 2722 peptides, 418 chains. Longest chain 22 peptides. Score 0.437 Round 4: 2681 peptides, 399 chains. Longest chain 24 peptides. Score 0.447 Round 5: 2704 peptides, 396 chains. Longest chain 24 peptides. Score 0.454 Taking the results from Round 5 Chains 397, Residues 2308, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 63786 reflections ( 92.90 % complete ) and 8863 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1878 (Rfree = 0.000) for 37165 atoms. Found 204 (204 requested) and removed 131 (102 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.1818 (Rfree = 0.000) for 37238 atoms. Found 204 (204 requested) and removed 143 (102 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1743 (Rfree = 0.000) for 37299 atoms. Found 205 (205 requested) and removed 161 (102 requested) atoms. Cycle 39: After refmac, R = 0.1686 (Rfree = 0.000) for 37343 atoms. Found 205 (205 requested) and removed 157 (102 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1637 (Rfree = 0.000) for 37391 atoms. Found 205 (205 requested) and removed 168 (102 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.62 3.12 Search for helices and strands: 0 residues in 0 chains, 38899 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 38915 seeds are put forward Round 1: 2136 peptides, 421 chains. Longest chain 14 peptides. Score 0.293 Round 2: 2543 peptides, 411 chains. Longest chain 25 peptides. Score 0.404 Round 3: 2589 peptides, 415 chains. Longest chain 20 peptides. Score 0.410 Round 4: 2610 peptides, 403 chains. Longest chain 25 peptides. Score 0.427 Round 5: 2654 peptides, 406 chains. Longest chain 25 peptides. Score 0.434 Taking the results from Round 5 Chains 407, Residues 2248, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 63786 reflections ( 92.90 % complete ) and 8682 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1779 (Rfree = 0.000) for 37165 atoms. Found 204 (204 requested) and removed 152 (102 requested) atoms. Cycle 42: After refmac, R = 0.1343 (Rfree = 0.000) for 37217 atoms. Found 46 (204 requested) and removed 125 (102 requested) atoms. Cycle 43: After refmac, R = 0.1221 (Rfree = 0.000) for 37138 atoms. Found 20 (204 requested) and removed 124 (102 requested) atoms. Cycle 44: After refmac, R = 0.1184 (Rfree = 0.000) for 37034 atoms. Found 24 (203 requested) and removed 107 (101 requested) atoms. Cycle 45: After refmac, R = 0.1163 (Rfree = 0.000) for 36951 atoms. Found 17 (203 requested) and removed 106 (101 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.65 3.14 Search for helices and strands: 0 residues in 0 chains, 38092 seeds are put forward NCS extension: 32 residues added (0 deleted due to clashes), 38124 seeds are put forward Round 1: 2119 peptides, 417 chains. Longest chain 15 peptides. Score 0.293 Round 2: 2408 peptides, 402 chains. Longest chain 18 peptides. Score 0.381 Round 3: 2498 peptides, 402 chains. Longest chain 21 peptides. Score 0.402 Round 4: 2512 peptides, 380 chains. Longest chain 23 peptides. Score 0.428 Round 5: 2525 peptides, 390 chains. Longest chain 18 peptides. Score 0.421 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 383, Residues 2132, Estimated correctness of the model 0.0 % 4 chains (45 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 2pnk-3_warpNtrace.pdb as input Building loops using Loopy2018 383 chains (2132 residues) following loop building 4 chains (45 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 63786 reflections ( 92.90 % complete ) and 8333 restraints for refining 37165 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1764 (Rfree = 0.000) for 37165 atoms. Found 0 (204 requested) and removed 102 (102 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.1772 (Rfree = 0.000) for 37063 atoms. Found 0 (203 requested) and removed 101 (101 requested) atoms. Cycle 48: After refmac, R = 0.1304 (Rfree = 0.000) for 36962 atoms. Found 0 (203 requested) and removed 101 (101 requested) atoms. Cycle 49: After refmac, R = 0.1197 (Rfree = 0.000) for 36861 atoms. Found 0 (202 requested) and removed 101 (101 requested) atoms. Writing output files ... TimeTaking 391.6