Sun 23 Dec 22:23:10 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 2pke-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pke-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pke-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pke-3.2-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/2pke-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pke-3.2-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 22:23:19 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/2pke-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pke-3.2-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 307 and 0 Target number of residues in the AU: 307 Target solvent content: 0.6303 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-3.2-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: 4 Cell parameters: 34.220 107.280 62.650 90.000 102.296 90.000 Input sequence file: 2pke-3.2-parrot-hancs.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 3.200 Wilson plot Bfac: 66.17 7099 reflections ( 96.62 % complete ) and 0 restraints for refining 4452 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.2987 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2692 (Rfree = 0.000) for 4452 atoms. Found 39 (39 requested) and removed 44 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.20 3.66 Search for helices and strands: 0 residues in 0 chains, 4548 seeds are put forward NCS extension: 0 residues added, 4548 seeds are put forward Round 1: 219 peptides, 46 chains. Longest chain 9 peptides. Score 0.304 Round 2: 253 peptides, 39 chains. Longest chain 15 peptides. Score 0.519 Round 3: 263 peptides, 34 chains. Longest chain 18 peptides. Score 0.609 Round 4: 291 peptides, 42 chains. Longest chain 19 peptides. Score 0.590 Round 5: 278 peptides, 34 chains. Longest chain 17 peptides. Score 0.646 Taking the results from Round 5 Chains 36, Residues 244, Estimated correctness of the model 52.9 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 7099 reflections ( 96.62 % complete ) and 8118 restraints for refining 3665 atoms. 7069 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2449 (Rfree = 0.000) for 3665 atoms. Found 20 (32 requested) and removed 80 (16 requested) atoms. Cycle 2: After refmac, R = 0.2253 (Rfree = 0.000) for 3584 atoms. Found 19 (32 requested) and removed 23 (16 requested) atoms. Cycle 3: After refmac, R = 0.2129 (Rfree = 0.000) for 3564 atoms. Found 17 (32 requested) and removed 24 (16 requested) atoms. Cycle 4: After refmac, R = 0.2636 (Rfree = 0.000) for 3547 atoms. Found 31 (31 requested) and removed 21 (15 requested) atoms. Cycle 5: After refmac, R = 0.2106 (Rfree = 0.000) for 3548 atoms. Found 27 (31 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.15 3.61 Search for helices and strands: 0 residues in 0 chains, 3692 seeds are put forward NCS extension: 10 residues added (4 deleted due to clashes), 3702 seeds are put forward Round 1: 264 peptides, 45 chains. Longest chain 16 peptides. Score 0.474 Round 2: 290 peptides, 38 chains. Longest chain 23 peptides. Score 0.632 Round 3: 273 peptides, 39 chains. Longest chain 22 peptides. Score 0.577 Round 4: 280 peptides, 39 chains. Longest chain 19 peptides. Score 0.595 Round 5: 276 peptides, 39 chains. Longest chain 19 peptides. Score 0.585 Taking the results from Round 2 Chains 42, Residues 252, Estimated correctness of the model 49.4 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 7099 reflections ( 96.62 % complete ) and 7919 restraints for refining 3549 atoms. 6883 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2421 (Rfree = 0.000) for 3549 atoms. Found 31 (31 requested) and removed 105 (15 requested) atoms. Cycle 7: After refmac, R = 0.1995 (Rfree = 0.000) for 3459 atoms. Found 28 (31 requested) and removed 38 (15 requested) atoms. Cycle 8: After refmac, R = 0.2386 (Rfree = 0.000) for 3432 atoms. Found 30 (30 requested) and removed 21 (15 requested) atoms. Cycle 9: After refmac, R = 0.1937 (Rfree = 0.000) for 3430 atoms. Found 26 (30 requested) and removed 29 (15 requested) atoms. Cycle 10: After refmac, R = 0.1985 (Rfree = 0.000) for 3421 atoms. Found 30 (30 requested) and removed 25 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.08 3.53 Search for helices and strands: 0 residues in 0 chains, 3581 seeds are put forward NCS extension: 28 residues added (5 deleted due to clashes), 3609 seeds are put forward Round 1: 204 peptides, 36 chains. Longest chain 12 peptides. Score 0.402 Round 2: 247 peptides, 39 chains. Longest chain 14 peptides. Score 0.501 Round 3: 232 peptides, 38 chains. Longest chain 14 peptides. Score 0.468 Round 4: 235 peptides, 35 chains. Longest chain 22 peptides. Score 0.518 Round 5: 247 peptides, 38 chains. Longest chain 23 peptides. Score 0.514 Taking the results from Round 4 Chains 39, Residues 200, Estimated correctness of the model 17.1 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 7099 reflections ( 96.62 % complete ) and 8192 restraints for refining 3571 atoms. 7338 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2010 (Rfree = 0.000) for 3571 atoms. Found 24 (32 requested) and removed 30 (16 requested) atoms. Cycle 12: After refmac, R = 0.2056 (Rfree = 0.000) for 3555 atoms. Found 31 (31 requested) and removed 29 (15 requested) atoms. Cycle 13: After refmac, R = 0.2103 (Rfree = 0.000) for 3546 atoms. Found 31 (31 requested) and removed 22 (15 requested) atoms. Cycle 14: After refmac, R = 0.1791 (Rfree = 0.000) for 3545 atoms. Found 22 (31 requested) and removed 19 (15 requested) atoms. Cycle 15: After refmac, R = 0.1676 (Rfree = 0.000) for 3537 atoms. Found 23 (31 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.16 3.62 Search for helices and strands: 0 residues in 0 chains, 3699 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3717 seeds are put forward Round 1: 189 peptides, 34 chains. Longest chain 16 peptides. Score 0.379 Round 2: 235 peptides, 40 chains. Longest chain 11 peptides. Score 0.449 Round 3: 259 peptides, 38 chains. Longest chain 20 peptides. Score 0.550 Round 4: 245 peptides, 34 chains. Longest chain 15 peptides. Score 0.560 Round 5: 251 peptides, 38 chains. Longest chain 16 peptides. Score 0.527 Taking the results from Round 4 Chains 34, Residues 211, Estimated correctness of the model 29.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7099 reflections ( 96.62 % complete ) and 8167 restraints for refining 3505 atoms. 7357 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2147 (Rfree = 0.000) for 3505 atoms. Found 25 (31 requested) and removed 26 (15 requested) atoms. Cycle 17: After refmac, R = 0.1910 (Rfree = 0.000) for 3495 atoms. Found 31 (31 requested) and removed 24 (15 requested) atoms. Cycle 18: After refmac, R = 0.1780 (Rfree = 0.000) for 3496 atoms. Found 23 (31 requested) and removed 21 (15 requested) atoms. Cycle 19: After refmac, R = 0.2294 (Rfree = 0.000) for 3491 atoms. Found 31 (31 requested) and removed 23 (15 requested) atoms. Cycle 20: After refmac, R = 0.1967 (Rfree = 0.000) for 3495 atoms. Found 31 (31 requested) and removed 23 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.17 3.63 Search for helices and strands: 0 residues in 0 chains, 3687 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3708 seeds are put forward Round 1: 193 peptides, 34 chains. Longest chain 15 peptides. Score 0.393 Round 2: 225 peptides, 33 chains. Longest chain 16 peptides. Score 0.514 Round 3: 221 peptides, 34 chains. Longest chain 14 peptides. Score 0.488 Round 4: 249 peptides, 38 chains. Longest chain 21 peptides. Score 0.521 Round 5: 243 peptides, 40 chains. Longest chain 14 peptides. Score 0.475 Taking the results from Round 4 Chains 39, Residues 211, Estimated correctness of the model 18.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7099 reflections ( 96.62 % complete ) and 8311 restraints for refining 3592 atoms. 7476 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1850 (Rfree = 0.000) for 3592 atoms. Found 21 (32 requested) and removed 23 (16 requested) atoms. Cycle 22: After refmac, R = 0.1753 (Rfree = 0.000) for 3581 atoms. Found 27 (32 requested) and removed 21 (16 requested) atoms. Cycle 23: After refmac, R = 0.1803 (Rfree = 0.000) for 3579 atoms. Found 14 (32 requested) and removed 20 (16 requested) atoms. Cycle 24: After refmac, R = 0.1619 (Rfree = 0.000) for 3567 atoms. Found 10 (32 requested) and removed 17 (16 requested) atoms. Cycle 25: After refmac, R = 0.1459 (Rfree = 0.000) for 3560 atoms. Found 1 (31 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.22 3.69 Search for helices and strands: 0 residues in 0 chains, 3715 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 3732 seeds are put forward Round 1: 170 peptides, 31 chains. Longest chain 12 peptides. Score 0.356 Round 2: 208 peptides, 30 chains. Longest chain 16 peptides. Score 0.502 Round 3: 238 peptides, 36 chains. Longest chain 12 peptides. Score 0.514 Round 4: 233 peptides, 36 chains. Longest chain 12 peptides. Score 0.498 Round 5: 228 peptides, 33 chains. Longest chain 19 peptides. Score 0.523 Taking the results from Round 5 Chains 35, Residues 195, Estimated correctness of the model 18.7 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 7099 reflections ( 96.62 % complete ) and 8369 restraints for refining 3636 atoms. 7535 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2085 (Rfree = 0.000) for 3636 atoms. Found 32 (32 requested) and removed 40 (16 requested) atoms. Cycle 27: After refmac, R = 0.1859 (Rfree = 0.000) for 3622 atoms. Found 32 (32 requested) and removed 28 (16 requested) atoms. Cycle 28: After refmac, R = 0.1893 (Rfree = 0.000) for 3618 atoms. Found 32 (32 requested) and removed 26 (16 requested) atoms. Cycle 29: After refmac, R = 0.1741 (Rfree = 0.000) for 3611 atoms. Found 28 (32 requested) and removed 25 (16 requested) atoms. Cycle 30: After refmac, R = 0.1692 (Rfree = 0.000) for 3609 atoms. Found 16 (32 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.20 3.66 Search for helices and strands: 0 residues in 0 chains, 3730 seeds are put forward NCS extension: 9 residues added (3 deleted due to clashes), 3739 seeds are put forward Round 1: 162 peptides, 30 chains. Longest chain 11 peptides. Score 0.342 Round 2: 192 peptides, 32 chains. Longest chain 11 peptides. Score 0.420 Round 3: 203 peptides, 34 chains. Longest chain 11 peptides. Score 0.428 Round 4: 189 peptides, 30 chains. Longest chain 11 peptides. Score 0.440 Round 5: 192 peptides, 29 chains. Longest chain 15 peptides. Score 0.465 Taking the results from Round 5 Chains 29, Residues 163, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7099 reflections ( 96.62 % complete ) and 8679 restraints for refining 3629 atoms. 8025 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1940 (Rfree = 0.000) for 3629 atoms. Found 32 (32 requested) and removed 23 (16 requested) atoms. Cycle 32: After refmac, R = 0.1820 (Rfree = 0.000) for 3635 atoms. Failed to save intermediate PDB Found 23 (32 requested) and removed 25 (16 requested) atoms. Cycle 33: After refmac, R = 0.2320 (Rfree = 0.000) for 3627 atoms. Found 32 (32 requested) and removed 19 (16 requested) atoms. Cycle 34: After refmac, R = 0.1815 (Rfree = 0.000) for 3633 atoms. Found 20 (32 requested) and removed 17 (16 requested) atoms. Cycle 35: After refmac, R = 0.1553 (Rfree = 0.000) for 3632 atoms. Found 15 (32 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 3.63 Search for helices and strands: 0 residues in 0 chains, 3759 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 3762 seeds are put forward Round 1: 157 peptides, 32 chains. Longest chain 8 peptides. Score 0.289 Round 2: 186 peptides, 31 chains. Longest chain 14 peptides. Score 0.414 Round 3: 187 peptides, 30 chains. Longest chain 17 peptides. Score 0.433 Round 4: 193 peptides, 31 chains. Longest chain 17 peptides. Score 0.439 Round 5: 194 peptides, 33 chains. Longest chain 12 peptides. Score 0.412 Taking the results from Round 4 Chains 33, Residues 162, Estimated correctness of the model 0.0 % 4 chains (33 residues) have been docked in sequence ------------------------------------------------------ 7099 reflections ( 96.62 % complete ) and 8494 restraints for refining 3663 atoms. 7753 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2021 (Rfree = 0.000) for 3663 atoms. Found 32 (32 requested) and removed 26 (16 requested) atoms. Cycle 37: After refmac, R = 0.2278 (Rfree = 0.000) for 3659 atoms. Found 32 (32 requested) and removed 22 (16 requested) atoms. Cycle 38: After refmac, R = 0.2816 (Rfree = 0.000) for 3657 atoms. Found 32 (32 requested) and removed 56 (16 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2260 (Rfree = 0.000) for 3614 atoms. Found 32 (32 requested) and removed 25 (16 requested) atoms. Cycle 40: After refmac, R = 0.2163 (Rfree = 0.000) for 3607 atoms. Found 32 (32 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.15 3.61 Search for helices and strands: 0 residues in 0 chains, 3779 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3794 seeds are put forward Round 1: 123 peptides, 25 chains. Longest chain 9 peptides. Score 0.271 Round 2: 145 peptides, 27 chains. Longest chain 10 peptides. Score 0.326 Round 3: 175 peptides, 30 chains. Longest chain 10 peptides. Score 0.391 Round 4: 165 peptides, 30 chains. Longest chain 11 peptides. Score 0.353 Round 5: 173 peptides, 29 chains. Longest chain 10 peptides. Score 0.399 Taking the results from Round 5 Chains 29, Residues 144, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7099 reflections ( 96.62 % complete ) and 8179 restraints for refining 3484 atoms. 7618 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2177 (Rfree = 0.000) for 3484 atoms. Found 27 (31 requested) and removed 20 (15 requested) atoms. Cycle 42: After refmac, R = 0.2156 (Rfree = 0.000) for 3482 atoms. Found 31 (31 requested) and removed 21 (15 requested) atoms. Cycle 43: After refmac, R = 0.1988 (Rfree = 0.000) for 3483 atoms. Found 31 (31 requested) and removed 19 (15 requested) atoms. Cycle 44: After refmac, R = 0.1793 (Rfree = 0.000) for 3488 atoms. Found 26 (31 requested) and removed 18 (15 requested) atoms. Cycle 45: After refmac, R = 0.1720 (Rfree = 0.000) for 3487 atoms. Found 23 (31 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.17 3.63 Search for helices and strands: 0 residues in 0 chains, 3623 seeds are put forward NCS extension: 0 residues added, 3623 seeds are put forward Round 1: 127 peptides, 25 chains. Longest chain 10 peptides. Score 0.288 Round 2: 160 peptides, 27 chains. Longest chain 12 peptides. Score 0.383 Round 3: 156 peptides, 28 chains. Longest chain 12 peptides. Score 0.352 Round 4: 167 peptides, 29 chains. Longest chain 12 peptides. Score 0.377 Round 5: 158 peptides, 28 chains. Longest chain 12 peptides. Score 0.360 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 133, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2pke-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7099 reflections ( 96.62 % complete ) and 7942 restraints for refining 3416 atoms. 7403 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1832 (Rfree = 0.000) for 3416 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.1741 (Rfree = 0.000) for 3394 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.1680 (Rfree = 0.000) for 3376 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.1717 (Rfree = 0.000) for 3360 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 55.52