Mon 24 Dec 01:11:49 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 2pke-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pke-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pke-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pke-3.6-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/2pke-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pke-3.6-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 01:11:53 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/2pke-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pke-3.6-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 291 and 0 Target number of residues in the AU: 291 Target solvent content: 0.6496 Checking the provided sequence file Detected sequence length: 251 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 502 Adjusted target solvent content: 0.40 Input MTZ file: 2pke-3.6-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: 4 Cell parameters: 34.220 107.280 62.650 90.000 102.296 90.000 Input sequence file: 2pke-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4016 target number of atoms Had to go as low as 0.50 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: 61.213 3.600 Wilson plot Bfac: 77.87 4971 reflections ( 96.02 % complete ) and 0 restraints for refining 4435 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3009 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2672 (Rfree = 0.000) for 4435 atoms. Found 28 (28 requested) and removed 50 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.55 4.06 Search for helices and strands: 0 residues in 0 chains, 4523 seeds are put forward NCS extension: 0 residues added, 4523 seeds are put forward Round 1: 172 peptides, 34 chains. Longest chain 13 peptides. Score 0.315 Round 2: 231 peptides, 39 chains. Longest chain 12 peptides. Score 0.450 Round 3: 246 peptides, 37 chains. Longest chain 14 peptides. Score 0.525 Round 4: 250 peptides, 36 chains. Longest chain 19 peptides. Score 0.549 Round 5: 252 peptides, 35 chains. Longest chain 22 peptides. Score 0.567 Taking the results from Round 5 Chains 37, Residues 217, Estimated correctness of the model 1.3 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 4971 reflections ( 96.02 % complete ) and 8428 restraints for refining 3641 atoms. 7525 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2043 (Rfree = 0.000) for 3641 atoms. Found 16 (23 requested) and removed 41 (11 requested) atoms. Cycle 2: After refmac, R = 0.1804 (Rfree = 0.000) for 3579 atoms. Found 15 (23 requested) and removed 17 (11 requested) atoms. Cycle 3: After refmac, R = 0.1927 (Rfree = 0.000) for 3562 atoms. Found 15 (22 requested) and removed 21 (11 requested) atoms. Cycle 4: After refmac, R = 0.1612 (Rfree = 0.000) for 3545 atoms. Found 8 (22 requested) and removed 17 (11 requested) atoms. Cycle 5: After refmac, R = 0.1644 (Rfree = 0.000) for 3532 atoms. Found 15 (22 requested) and removed 21 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 3.89 Search for helices and strands: 0 residues in 0 chains, 3715 seeds are put forward NCS extension: 8 residues added (1 deleted due to clashes), 3723 seeds are put forward Round 1: 196 peptides, 37 chains. Longest chain 11 peptides. Score 0.358 Round 2: 218 peptides, 36 chains. Longest chain 15 peptides. Score 0.450 Round 3: 226 peptides, 35 chains. Longest chain 15 peptides. Score 0.490 Round 4: 240 peptides, 34 chains. Longest chain 17 peptides. Score 0.546 Round 5: 234 peptides, 31 chains. Longest chain 15 peptides. Score 0.567 Taking the results from Round 5 Chains 31, Residues 203, Estimated correctness of the model 1.3 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 4971 reflections ( 96.02 % complete ) and 8355 restraints for refining 3609 atoms. 7491 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2001 (Rfree = 0.000) for 3609 atoms. Found 20 (23 requested) and removed 41 (11 requested) atoms. Cycle 7: After refmac, R = 0.2430 (Rfree = 0.000) for 3575 atoms. Found 23 (23 requested) and removed 150 (11 requested) atoms. Cycle 8: After refmac, R = 0.1841 (Rfree = 0.000) for 3438 atoms. Found 16 (22 requested) and removed 41 (11 requested) atoms. Cycle 9: After refmac, R = 0.1837 (Rfree = 0.000) for 3406 atoms. Found 14 (21 requested) and removed 21 (10 requested) atoms. Cycle 10: After refmac, R = 0.1738 (Rfree = 0.000) for 3398 atoms. Found 13 (21 requested) and removed 20 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.93 Search for helices and strands: 0 residues in 0 chains, 3580 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 3594 seeds are put forward Round 1: 196 peptides, 38 chains. Longest chain 13 peptides. Score 0.342 Round 2: 218 peptides, 35 chains. Longest chain 13 peptides. Score 0.464 Round 3: 211 peptides, 30 chains. Longest chain 16 peptides. Score 0.512 Round 4: 228 peptides, 31 chains. Longest chain 16 peptides. Score 0.549 Round 5: 240 peptides, 29 chains. Longest chain 25 peptides. Score 0.608 Taking the results from Round 5 Chains 30, Residues 211, Estimated correctness of the model 17.8 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4971 reflections ( 96.02 % complete ) and 8133 restraints for refining 3543 atoms. 7283 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1723 (Rfree = 0.000) for 3543 atoms. Found 22 (22 requested) and removed 54 (11 requested) atoms. Cycle 12: After refmac, R = 0.1682 (Rfree = 0.000) for 3492 atoms. Found 22 (22 requested) and removed 26 (11 requested) atoms. Cycle 13: After refmac, R = 0.1644 (Rfree = 0.000) for 3481 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. Cycle 14: After refmac, R = 0.1594 (Rfree = 0.000) for 3472 atoms. Found 20 (22 requested) and removed 28 (11 requested) atoms. Cycle 15: After refmac, R = 0.1591 (Rfree = 0.000) for 3462 atoms. Found 14 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.48 3.98 Search for helices and strands: 0 residues in 0 chains, 3606 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 3632 seeds are put forward Round 1: 162 peptides, 34 chains. Longest chain 10 peptides. Score 0.276 Round 2: 181 peptides, 32 chains. Longest chain 13 peptides. Score 0.381 Round 3: 189 peptides, 33 chains. Longest chain 13 peptides. Score 0.394 Round 4: 189 peptides, 30 chains. Longest chain 16 peptides. Score 0.440 Round 5: 191 peptides, 29 chains. Longest chain 13 peptides. Score 0.462 Taking the results from Round 5 Chains 29, Residues 162, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4971 reflections ( 96.02 % complete ) and 8545 restraints for refining 3558 atoms. 7894 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1774 (Rfree = 0.000) for 3558 atoms. Found 22 (22 requested) and removed 41 (11 requested) atoms. Cycle 17: After refmac, R = 0.1705 (Rfree = 0.000) for 3523 atoms. Found 22 (22 requested) and removed 49 (11 requested) atoms. Cycle 18: After refmac, R = 0.1662 (Rfree = 0.000) for 3488 atoms. Found 22 (22 requested) and removed 31 (11 requested) atoms. Cycle 19: After refmac, R = 0.1620 (Rfree = 0.000) for 3477 atoms. Found 22 (22 requested) and removed 16 (11 requested) atoms. Cycle 20: After refmac, R = 0.1381 (Rfree = 0.000) for 3479 atoms. Found 6 (22 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 3.97 Search for helices and strands: 0 residues in 0 chains, 3611 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3627 seeds are put forward Round 1: 160 peptides, 35 chains. Longest chain 8 peptides. Score 0.251 Round 2: 185 peptides, 37 chains. Longest chain 9 peptides. Score 0.317 Round 3: 169 peptides, 32 chains. Longest chain 9 peptides. Score 0.336 Round 4: 168 peptides, 30 chains. Longest chain 9 peptides. Score 0.365 Round 5: 170 peptides, 30 chains. Longest chain 9 peptides. Score 0.372 Taking the results from Round 5 Chains 30, Residues 140, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4971 reflections ( 96.02 % complete ) and 8958 restraints for refining 3554 atoms. 8400 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1712 (Rfree = 0.000) for 3554 atoms. Found 11 (22 requested) and removed 60 (11 requested) atoms. Cycle 22: After refmac, R = 0.1752 (Rfree = 0.000) for 3496 atoms. Found 22 (22 requested) and removed 29 (11 requested) atoms. Cycle 23: After refmac, R = 0.1566 (Rfree = 0.000) for 3486 atoms. Found 21 (22 requested) and removed 24 (11 requested) atoms. Cycle 24: After refmac, R = 0.1548 (Rfree = 0.000) for 3482 atoms. Found 18 (22 requested) and removed 17 (11 requested) atoms. Cycle 25: After refmac, R = 0.1564 (Rfree = 0.000) for 3483 atoms. Found 17 (22 requested) and removed 18 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 3.94 Search for helices and strands: 0 residues in 0 chains, 3618 seeds are put forward NCS extension: 0 residues added, 3618 seeds are put forward Round 1: 148 peptides, 32 chains. Longest chain 8 peptides. Score 0.253 Round 2: 173 peptides, 32 chains. Longest chain 9 peptides. Score 0.351 Round 3: 170 peptides, 32 chains. Longest chain 10 peptides. Score 0.340 Round 4: 178 peptides, 32 chains. Longest chain 11 peptides. Score 0.370 Round 5: 176 peptides, 30 chains. Longest chain 12 peptides. Score 0.394 Taking the results from Round 5 Chains 30, Residues 146, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4971 reflections ( 96.02 % complete ) and 8594 restraints for refining 3564 atoms. 8019 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1754 (Rfree = 0.000) for 3564 atoms. Found 15 (22 requested) and removed 45 (11 requested) atoms. Cycle 27: After refmac, R = 0.1630 (Rfree = 0.000) for 3527 atoms. Found 18 (22 requested) and removed 43 (11 requested) atoms. Cycle 28: After refmac, R = 0.1607 (Rfree = 0.000) for 3500 atoms. Found 19 (22 requested) and removed 20 (11 requested) atoms. Cycle 29: After refmac, R = 0.1260 (Rfree = 0.000) for 3492 atoms. Found 1 (22 requested) and removed 15 (11 requested) atoms. Cycle 30: After refmac, R = 0.1194 (Rfree = 0.000) for 3476 atoms. Found 2 (22 requested) and removed 18 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.49 3.99 Search for helices and strands: 0 residues in 0 chains, 3601 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3616 seeds are put forward Round 1: 143 peptides, 31 chains. Longest chain 9 peptides. Score 0.249 Round 2: 161 peptides, 31 chains. Longest chain 10 peptides. Score 0.322 Round 3: 168 peptides, 31 chains. Longest chain 9 peptides. Score 0.349 Round 4: 171 peptides, 32 chains. Longest chain 10 peptides. Score 0.344 Round 5: 174 peptides, 31 chains. Longest chain 12 peptides. Score 0.371 Taking the results from Round 5 Chains 31, Residues 143, Estimated correctness of the model 0.0 % 5 chains (27 residues) have been docked in sequence ------------------------------------------------------ 4971 reflections ( 96.02 % complete ) and 8439 restraints for refining 3583 atoms. 7823 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1604 (Rfree = 0.000) for 3583 atoms. Found 19 (22 requested) and removed 37 (11 requested) atoms. Cycle 32: After refmac, R = 0.1648 (Rfree = 0.000) for 3552 atoms. Found 19 (22 requested) and removed 17 (11 requested) atoms. Cycle 33: After refmac, R = 0.1622 (Rfree = 0.000) for 3548 atoms. Found 21 (22 requested) and removed 14 (11 requested) atoms. Cycle 34: After refmac, R = 0.1597 (Rfree = 0.000) for 3546 atoms. Found 21 (22 requested) and removed 14 (11 requested) atoms. Cycle 35: After refmac, R = 0.1487 (Rfree = 0.000) for 3548 atoms. Found 16 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.44 3.94 Search for helices and strands: 0 residues in 0 chains, 3689 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3708 seeds are put forward Round 1: 138 peptides, 30 chains. Longest chain 8 peptides. Score 0.246 Round 2: 181 peptides, 33 chains. Longest chain 12 peptides. Score 0.365 Round 3: 166 peptides, 29 chains. Longest chain 10 peptides. Score 0.373 Round 4: 174 peptides, 28 chains. Longest chain 10 peptides. Score 0.418 Round 5: 180 peptides, 28 chains. Longest chain 11 peptides. Score 0.439 Taking the results from Round 5 Chains 28, Residues 152, Estimated correctness of the model 0.0 % 6 chains (32 residues) have been docked in sequence ------------------------------------------------------ 4971 reflections ( 96.02 % complete ) and 8648 restraints for refining 3640 atoms. 7979 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1727 (Rfree = 0.000) for 3640 atoms. Found 23 (23 requested) and removed 18 (11 requested) atoms. Cycle 37: After refmac, R = 0.1712 (Rfree = 0.000) for 3637 atoms. Found 23 (23 requested) and removed 21 (11 requested) atoms. Cycle 38: After refmac, R = 0.1615 (Rfree = 0.000) for 3635 atoms. Found 23 (23 requested) and removed 17 (11 requested) atoms. Cycle 39: After refmac, R = 0.1582 (Rfree = 0.000) for 3633 atoms. Found 23 (23 requested) and removed 17 (11 requested) atoms. Cycle 40: After refmac, R = 0.1464 (Rfree = 0.000) for 3634 atoms. Found 18 (23 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.49 3.99 Search for helices and strands: 0 residues in 0 chains, 3784 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 3787 seeds are put forward Round 1: 137 peptides, 29 chains. Longest chain 8 peptides. Score 0.259 Round 2: 164 peptides, 30 chains. Longest chain 9 peptides. Score 0.350 Round 3: 167 peptides, 30 chains. Longest chain 12 peptides. Score 0.361 Round 4: 170 peptides, 31 chains. Longest chain 11 peptides. Score 0.356 Round 5: 179 peptides, 30 chains. Longest chain 11 peptides. Score 0.405 Taking the results from Round 5 Chains 30, Residues 149, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4971 reflections ( 96.02 % complete ) and 9013 restraints for refining 3641 atoms. 8447 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1729 (Rfree = 0.000) for 3641 atoms. Found 23 (23 requested) and removed 27 (11 requested) atoms. Cycle 42: After refmac, R = 0.1668 (Rfree = 0.000) for 3625 atoms. Found 23 (23 requested) and removed 19 (11 requested) atoms. Cycle 43: After refmac, R = 0.1637 (Rfree = 0.000) for 3622 atoms. Found 23 (23 requested) and removed 17 (11 requested) atoms. Cycle 44: After refmac, R = 0.1503 (Rfree = 0.000) for 3623 atoms. Found 23 (23 requested) and removed 13 (11 requested) atoms. Cycle 45: After refmac, R = 0.1609 (Rfree = 0.000) for 3631 atoms. Found 23 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.44 3.94 Search for helices and strands: 0 residues in 0 chains, 3771 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 3782 seeds are put forward Round 1: 143 peptides, 32 chains. Longest chain 11 peptides. Score 0.232 Round 2: 157 peptides, 32 chains. Longest chain 11 peptides. Score 0.289 Round 3: 146 peptides, 26 chains. Longest chain 17 peptides. Score 0.347 Round 4: 150 peptides, 27 chains. Longest chain 17 peptides. Score 0.346 Round 5: 149 peptides, 27 chains. Longest chain 12 peptides. Score 0.342 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 120, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2pke-3_warpNtrace.pdb as input Building loops using Loopy2018 26 chains (120 residues) following loop building 2 chains (8 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4971 reflections ( 96.02 % complete ) and 9071 restraints for refining 3641 atoms. 8594 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1644 (Rfree = 0.000) for 3641 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.1639 (Rfree = 0.000) for 3621 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.1485 (Rfree = 0.000) for 3604 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1505 (Rfree = 0.000) for 3590 atoms. TimeTaking 33.57