null Sun 23 Dec 22:22:59 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2i5i-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2i5i-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2i5i-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i5i-4.0-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2i5i-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i5i-4.0-parrot-hancs ############### 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 22:23:09 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/hancs/ArpWArp/wArpResults/WorkingDir/2i5i-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2i5i-4.0-parrot-hancs/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 346 and 0 Target number of residues in the AU: 346 Target solvent content: 0.6670 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-4.0-parrot-hancs.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-4.0-parrot-hancs.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 4.002 Wilson plot Bfac: 89.81 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 4552 reflections ( 98.94 % complete ) and 0 restraints for refining 4652 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.3481 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3213 (Rfree = 0.000) for 4652 atoms. Found 20 (22 requested) and removed 44 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.99 4.04 Search for helices and strands: 0 residues in 0 chains, 4648 seeds are put forward NCS extension: 0 residues added, 4648 seeds are put forward Round 1: 82 peptides, 19 chains. Longest chain 6 peptides. Score 0.194 Round 2: 112 peptides, 25 chains. Longest chain 7 peptides. Score 0.215 Round 3: 128 peptides, 27 chains. Longest chain 8 peptides. Score 0.244 Round 4: 145 peptides, 31 chains. Longest chain 7 peptides. Score 0.244 Round 5: 145 peptides, 31 chains. Longest chain 8 peptides. Score 0.244 Taking the results from Round 5 Chains 31, Residues 114, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4552 reflections ( 98.94 % complete ) and 9463 restraints for refining 3799 atoms. 9038 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2380 (Rfree = 0.000) for 3799 atoms. Found 9 (18 requested) and removed 31 (9 requested) atoms. Cycle 2: After refmac, R = 0.2120 (Rfree = 0.000) for 3717 atoms. Found 7 (17 requested) and removed 29 (8 requested) atoms. Cycle 3: After refmac, R = 0.1923 (Rfree = 0.000) for 3668 atoms. Found 9 (17 requested) and removed 18 (8 requested) atoms. Cycle 4: After refmac, R = 0.1833 (Rfree = 0.000) for 3645 atoms. Found 3 (17 requested) and removed 17 (8 requested) atoms. Cycle 5: After refmac, R = 0.1816 (Rfree = 0.000) for 3620 atoms. Found 2 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.78 3.83 Search for helices and strands: 0 residues in 0 chains, 3684 seeds are put forward NCS extension: 0 residues added, 3684 seeds are put forward Round 1: 122 peptides, 27 chains. Longest chain 8 peptides. Score 0.221 Round 2: 161 peptides, 32 chains. Longest chain 9 peptides. Score 0.285 Round 3: 152 peptides, 29 chains. Longest chain 11 peptides. Score 0.297 Round 4: 163 peptides, 31 chains. Longest chain 9 peptides. Score 0.305 Round 5: 161 peptides, 32 chains. Longest chain 9 peptides. Score 0.285 Taking the results from Round 4 Chains 31, Residues 132, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4552 reflections ( 98.94 % complete ) and 8213 restraints for refining 3445 atoms. 7716 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1941 (Rfree = 0.000) for 3445 atoms. Found 16 (16 requested) and removed 32 (8 requested) atoms. Cycle 7: After refmac, R = 0.1757 (Rfree = 0.000) for 3414 atoms. Found 9 (16 requested) and removed 22 (8 requested) atoms. Cycle 8: After refmac, R = 0.1605 (Rfree = 0.000) for 3394 atoms. Found 7 (16 requested) and removed 13 (8 requested) atoms. Cycle 9: After refmac, R = 0.1660 (Rfree = 0.000) for 3382 atoms. Found 5 (16 requested) and removed 15 (8 requested) atoms. Cycle 10: After refmac, R = 0.1672 (Rfree = 0.000) for 3369 atoms. Found 2 (15 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.82 3.87 Search for helices and strands: 0 residues in 0 chains, 3433 seeds are put forward NCS extension: 0 residues added, 3433 seeds are put forward Round 1: 152 peptides, 33 chains. Longest chain 12 peptides. Score 0.239 Round 2: 185 peptides, 35 chains. Longest chain 11 peptides. Score 0.321 Round 3: 193 peptides, 35 chains. Longest chain 15 peptides. Score 0.346 Round 4: 200 peptides, 35 chains. Longest chain 17 peptides. Score 0.367 Round 5: 190 peptides, 35 chains. Longest chain 12 peptides. Score 0.336 Taking the results from Round 4 Chains 35, Residues 165, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4552 reflections ( 98.94 % complete ) and 7912 restraints for refining 3507 atoms. 7287 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1845 (Rfree = 0.000) for 3507 atoms. Found 12 (16 requested) and removed 25 (8 requested) atoms. Cycle 12: After refmac, R = 0.1625 (Rfree = 0.000) for 3482 atoms. Found 6 (16 requested) and removed 17 (8 requested) atoms. Cycle 13: After refmac, R = 0.1587 (Rfree = 0.000) for 3458 atoms. Found 2 (16 requested) and removed 16 (8 requested) atoms. Cycle 14: After refmac, R = 0.1518 (Rfree = 0.000) for 3440 atoms. Found 4 (16 requested) and removed 12 (8 requested) atoms. Cycle 15: After refmac, R = 0.1481 (Rfree = 0.000) for 3429 atoms. Found 5 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.79 3.84 Search for helices and strands: 0 residues in 0 chains, 3492 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 3517 seeds are put forward Round 1: 184 peptides, 40 chains. Longest chain 10 peptides. Score 0.249 Round 2: 212 peptides, 41 chains. Longest chain 12 peptides. Score 0.325 Round 3: 212 peptides, 40 chains. Longest chain 12 peptides. Score 0.338 Round 4: 221 peptides, 41 chains. Longest chain 12 peptides. Score 0.353 Round 5: 217 peptides, 38 chains. Longest chain 13 peptides. Score 0.379 Taking the results from Round 5 Chains 38, Residues 179, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4552 reflections ( 98.94 % complete ) and 8297 restraints for refining 3666 atoms. 7601 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1820 (Rfree = 0.000) for 3666 atoms. Found 12 (17 requested) and removed 28 (8 requested) atoms. Cycle 17: After refmac, R = 0.1637 (Rfree = 0.000) for 3628 atoms. Found 4 (17 requested) and removed 19 (8 requested) atoms. Cycle 18: After refmac, R = 0.1557 (Rfree = 0.000) for 3596 atoms. Found 2 (17 requested) and removed 14 (8 requested) atoms. Cycle 19: After refmac, R = 0.1486 (Rfree = 0.000) for 3573 atoms. Found 6 (17 requested) and removed 14 (8 requested) atoms. Cycle 20: After refmac, R = 0.1482 (Rfree = 0.000) for 3564 atoms. Found 2 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.80 3.85 Search for helices and strands: 0 residues in 0 chains, 3617 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3637 seeds are put forward Round 1: 183 peptides, 39 chains. Longest chain 13 peptides. Score 0.260 Round 2: 201 peptides, 36 chains. Longest chain 11 peptides. Score 0.357 Round 3: 201 peptides, 36 chains. Longest chain 13 peptides. Score 0.357 Round 4: 193 peptides, 32 chains. Longest chain 15 peptides. Score 0.385 Round 5: 194 peptides, 32 chains. Longest chain 13 peptides. Score 0.388 Taking the results from Round 5 Chains 32, Residues 162, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4552 reflections ( 98.94 % complete ) and 8461 restraints for refining 3656 atoms. 7845 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1614 (Rfree = 0.000) for 3656 atoms. Found 16 (17 requested) and removed 29 (8 requested) atoms. Cycle 22: After refmac, R = 0.1703 (Rfree = 0.000) for 3631 atoms. Found 11 (17 requested) and removed 12 (8 requested) atoms. Cycle 23: After refmac, R = 0.1369 (Rfree = 0.000) for 3620 atoms. Found 8 (17 requested) and removed 16 (8 requested) atoms. Cycle 24: After refmac, R = 0.1295 (Rfree = 0.000) for 3604 atoms. Found 8 (17 requested) and removed 11 (8 requested) atoms. Cycle 25: After refmac, R = 0.1308 (Rfree = 0.000) for 3596 atoms. Found 5 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.80 3.85 Search for helices and strands: 0 residues in 0 chains, 3690 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3703 seeds are put forward Round 1: 158 peptides, 34 chains. Longest chain 10 peptides. Score 0.246 Round 2: 169 peptides, 32 chains. Longest chain 11 peptides. Score 0.311 Round 3: 167 peptides, 33 chains. Longest chain 10 peptides. Score 0.290 Round 4: 190 peptides, 35 chains. Longest chain 12 peptides. Score 0.336 Round 5: 185 peptides, 34 chains. Longest chain 11 peptides. Score 0.334 Taking the results from Round 4 Chains 35, Residues 155, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4552 reflections ( 98.94 % complete ) and 8222 restraints for refining 3605 atoms. 7637 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1573 (Rfree = 0.000) for 3605 atoms. Found 16 (17 requested) and removed 20 (8 requested) atoms. Cycle 27: After refmac, R = 0.1484 (Rfree = 0.000) for 3590 atoms. Found 5 (17 requested) and removed 14 (8 requested) atoms. Cycle 28: After refmac, R = 0.1480 (Rfree = 0.000) for 3571 atoms. Found 3 (16 requested) and removed 13 (8 requested) atoms. Cycle 29: After refmac, R = 0.1326 (Rfree = 0.000) for 3557 atoms. Found 7 (16 requested) and removed 16 (8 requested) atoms. Cycle 30: After refmac, R = 0.1384 (Rfree = 0.000) for 3546 atoms. Found 6 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.80 3.85 Search for helices and strands: 0 residues in 0 chains, 3639 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3654 seeds are put forward Round 1: 181 peptides, 37 chains. Longest chain 13 peptides. Score 0.281 Round 2: 173 peptides, 32 chains. Longest chain 15 peptides. Score 0.324 Round 3: 178 peptides, 32 chains. Longest chain 19 peptides. Score 0.339 Round 4: 175 peptides, 33 chains. Longest chain 12 peptides. Score 0.316 Round 5: 190 peptides, 35 chains. Longest chain 18 peptides. Score 0.336 Taking the results from Round 3 Chains 32, Residues 146, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4552 reflections ( 98.94 % complete ) and 8518 restraints for refining 3694 atoms. 7932 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1499 (Rfree = 0.000) for 3694 atoms. Found 6 (17 requested) and removed 27 (8 requested) atoms. Cycle 32: After refmac, R = 0.1713 (Rfree = 0.000) for 3664 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 33: After refmac, R = 0.1422 (Rfree = 0.000) for 3651 atoms. Found 7 (17 requested) and removed 10 (8 requested) atoms. Cycle 34: After refmac, R = 0.1651 (Rfree = 0.000) for 3638 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 35: After refmac, R = 0.1371 (Rfree = 0.000) for 3623 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.81 3.86 Search for helices and strands: 0 residues in 0 chains, 3711 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 3738 seeds are put forward Round 1: 118 peptides, 27 chains. Longest chain 10 peptides. Score 0.206 Round 2: 133 peptides, 25 chains. Longest chain 12 peptides. Score 0.292 Round 3: 134 peptides, 25 chains. Longest chain 16 peptides. Score 0.295 Round 4: 124 peptides, 23 chains. Longest chain 13 peptides. Score 0.291 Round 5: 135 peptides, 25 chains. Longest chain 9 peptides. Score 0.299 Taking the results from Round 5 Chains 25, Residues 110, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4552 reflections ( 98.94 % complete ) and 8588 restraints for refining 3643 atoms. 8173 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1520 (Rfree = 0.000) for 3643 atoms. Found 15 (17 requested) and removed 22 (8 requested) atoms. Cycle 37: After refmac, R = 0.1457 (Rfree = 0.000) for 3630 atoms. Found 12 (17 requested) and removed 16 (8 requested) atoms. Cycle 38: After refmac, R = 0.1236 (Rfree = 0.000) for 3618 atoms. Found 7 (17 requested) and removed 14 (8 requested) atoms. Cycle 39: After refmac, R = 0.1325 (Rfree = 0.000) for 3609 atoms. Found 12 (17 requested) and removed 17 (8 requested) atoms. Cycle 40: After refmac, R = 0.1249 (Rfree = 0.000) for 3602 atoms. Found 7 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.81 3.86 Search for helices and strands: 0 residues in 0 chains, 3678 seeds are put forward NCS extension: 0 residues added, 3678 seeds are put forward Round 1: 118 peptides, 28 chains. Longest chain 6 peptides. Score 0.190 Round 2: 135 peptides, 27 chains. Longest chain 8 peptides. Score 0.269 Round 3: 153 peptides, 29 chains. Longest chain 11 peptides. Score 0.301 Round 4: 144 peptides, 27 chains. Longest chain 9 peptides. Score 0.300 Round 5: 148 peptides, 28 chains. Longest chain 9 peptides. Score 0.298 Taking the results from Round 3 Chains 29, Residues 124, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4552 reflections ( 98.94 % complete ) and 8666 restraints for refining 3670 atoms. 8199 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1952 (Rfree = 0.000) for 3670 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. Cycle 42: After refmac, R = 0.1646 (Rfree = 0.000) for 3648 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 43: After refmac, R = 0.1738 (Rfree = 0.000) for 3632 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 44: After refmac, R = 0.1501 (Rfree = 0.000) for 3620 atoms. Found 16 (17 requested) and removed 13 (8 requested) atoms. Cycle 45: After refmac, R = 0.1682 (Rfree = 0.000) for 3616 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.80 3.85 Search for helices and strands: 0 residues in 0 chains, 3702 seeds are put forward NCS extension: 7 residues added (0 deleted due to clashes), 3709 seeds are put forward Round 1: 91 peptides, 20 chains. Longest chain 7 peptides. Score 0.215 Round 2: 104 peptides, 19 chains. Longest chain 11 peptides. Score 0.283 Round 3: 106 peptides, 19 chains. Longest chain 9 peptides. Score 0.290 Round 4: 106 peptides, 19 chains. Longest chain 11 peptides. Score 0.290 Round 5: 102 peptides, 18 chains. Longest chain 10 peptides. Score 0.292 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 84, 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-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4552 reflections ( 98.94 % complete ) and 8467 restraints for refining 3548 atoms. 8149 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1601 (Rfree = 0.000) for 3548 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.1646 (Rfree = 0.000) for 3537 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1530 (Rfree = 0.000) for 3525 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1186 (Rfree = 0.000) for 3515 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:20:53 GMT 2018 Job finished. TimeTaking 57.91 Used memory is bytes: 19017624