Sun 23 Dec 22:23:05 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 2it9-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2it9-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2it9-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2it9-4.0-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/2it9-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2it9-4.0-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 22:23:15 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/2it9-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2it9-4.0-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 378 and 0 Target number of residues in the AU: 378 Target solvent content: 0.6600 Checking the provided sequence file Detected sequence length: 127 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 508 Adjusted target solvent content: 0.54 Input MTZ file: 2it9-4.0-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: 19 Cell parameters: 59.723 81.014 124.347 90.000 90.000 90.000 Input sequence file: 2it9-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 4064 target number of atoms Had to go as low as 0.85 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: 67.879 4.000 Wilson plot Bfac: 84.33 5337 reflections ( 98.03 % complete ) and 0 restraints for refining 4498 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3900 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3226 (Rfree = 0.000) for 4498 atoms. Found 13 (21 requested) and removed 30 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.70 3.51 Search for helices and strands: 0 residues in 0 chains, 4550 seeds are put forward NCS extension: 0 residues added, 4550 seeds are put forward Round 1: 146 peptides, 27 chains. Longest chain 10 peptides. Score 0.300 Round 2: 215 peptides, 38 chains. Longest chain 15 peptides. Score 0.363 Round 3: 224 peptides, 34 chains. Longest chain 14 peptides. Score 0.435 Round 4: 214 peptides, 31 chains. Longest chain 14 peptides. Score 0.444 Round 5: 231 peptides, 38 chains. Longest chain 12 peptides. Score 0.407 Taking the results from Round 4 Chains 31, Residues 183, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5337 reflections ( 98.03 % complete ) and 8716 restraints for refining 3670 atoms. 8015 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2697 (Rfree = 0.000) for 3670 atoms. Found 12 (17 requested) and removed 24 (8 requested) atoms. Cycle 2: After refmac, R = 0.2639 (Rfree = 0.000) for 3609 atoms. Found 6 (17 requested) and removed 21 (8 requested) atoms. Cycle 3: After refmac, R = 0.2547 (Rfree = 0.000) for 3560 atoms. Found 8 (17 requested) and removed 19 (8 requested) atoms. Cycle 4: After refmac, R = 0.2548 (Rfree = 0.000) for 3521 atoms. Found 11 (16 requested) and removed 20 (8 requested) atoms. Cycle 5: After refmac, R = 0.2424 (Rfree = 0.000) for 3490 atoms. Found 7 (16 requested) and removed 19 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.75 3.56 Search for helices and strands: 0 residues in 0 chains, 3594 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3611 seeds are put forward Round 1: 179 peptides, 35 chains. Longest chain 12 peptides. Score 0.295 Round 2: 218 peptides, 34 chains. Longest chain 19 peptides. Score 0.419 Round 3: 226 peptides, 33 chains. Longest chain 19 peptides. Score 0.452 Round 4: 249 peptides, 38 chains. Longest chain 12 peptides. Score 0.454 Round 5: 239 peptides, 34 chains. Longest chain 14 peptides. Score 0.473 Taking the results from Round 5 Chains 34, Residues 205, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5337 reflections ( 98.03 % complete ) and 7885 restraints for refining 3456 atoms. 7099 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2457 (Rfree = 0.000) for 3456 atoms. Found 8 (16 requested) and removed 37 (8 requested) atoms. Cycle 7: After refmac, R = 0.2276 (Rfree = 0.000) for 3400 atoms. Found 3 (16 requested) and removed 20 (8 requested) atoms. Cycle 8: After refmac, R = 0.2252 (Rfree = 0.000) for 3374 atoms. Found 10 (16 requested) and removed 18 (8 requested) atoms. Cycle 9: After refmac, R = 0.2293 (Rfree = 0.000) for 3357 atoms. Found 5 (15 requested) and removed 17 (7 requested) atoms. Cycle 10: After refmac, R = 0.2157 (Rfree = 0.000) for 3334 atoms. Found 8 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.71 3.52 Search for helices and strands: 0 residues in 0 chains, 3455 seeds are put forward NCS extension: 0 residues added, 3455 seeds are put forward Round 1: 202 peptides, 39 chains. Longest chain 11 peptides. Score 0.313 Round 2: 219 peptides, 37 chains. Longest chain 13 peptides. Score 0.386 Round 3: 225 peptides, 35 chains. Longest chain 11 peptides. Score 0.426 Round 4: 219 peptides, 34 chains. Longest chain 14 peptides. Score 0.422 Round 5: 226 peptides, 35 chains. Longest chain 14 peptides. Score 0.429 Taking the results from Round 5 Chains 36, Residues 191, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5337 reflections ( 98.03 % complete ) and 8500 restraints for refining 3669 atoms. 7737 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2239 (Rfree = 0.000) for 3669 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. Cycle 12: After refmac, R = 0.2137 (Rfree = 0.000) for 3632 atoms. Found 10 (17 requested) and removed 27 (8 requested) atoms. Cycle 13: After refmac, R = 0.2029 (Rfree = 0.000) for 3608 atoms. Found 15 (17 requested) and removed 17 (8 requested) atoms. Cycle 14: After refmac, R = 0.1702 (Rfree = 0.000) for 3592 atoms. Found 4 (17 requested) and removed 12 (8 requested) atoms. Cycle 15: After refmac, R = 0.1718 (Rfree = 0.000) for 3577 atoms. Found 4 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.67 3.48 Search for helices and strands: 0 residues in 0 chains, 3657 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3671 seeds are put forward Round 1: 199 peptides, 40 chains. Longest chain 11 peptides. Score 0.292 Round 2: 225 peptides, 38 chains. Longest chain 13 peptides. Score 0.391 Round 3: 229 peptides, 36 chains. Longest chain 14 peptides. Score 0.425 Round 4: 239 peptides, 39 chains. Longest chain 15 peptides. Score 0.417 Round 5: 245 peptides, 37 chains. Longest chain 19 peptides. Score 0.455 Taking the results from Round 5 Chains 37, Residues 208, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5337 reflections ( 98.03 % complete ) and 8384 restraints for refining 3669 atoms. 7589 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2374 (Rfree = 0.000) for 3669 atoms. Found 8 (17 requested) and removed 17 (8 requested) atoms. Cycle 17: After refmac, R = 0.2092 (Rfree = 0.000) for 3644 atoms. Found 3 (17 requested) and removed 10 (8 requested) atoms. Cycle 18: After refmac, R = 0.2043 (Rfree = 0.000) for 3628 atoms. Found 5 (17 requested) and removed 12 (8 requested) atoms. Cycle 19: After refmac, R = 0.2004 (Rfree = 0.000) for 3618 atoms. Found 2 (17 requested) and removed 11 (8 requested) atoms. Cycle 20: After refmac, R = 0.1980 (Rfree = 0.000) for 3607 atoms. Found 4 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.70 3.51 Search for helices and strands: 0 residues in 0 chains, 3691 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3709 seeds are put forward Round 1: 196 peptides, 38 chains. Longest chain 9 peptides. Score 0.308 Round 2: 227 peptides, 36 chains. Longest chain 16 peptides. Score 0.420 Round 3: 213 peptides, 35 chains. Longest chain 12 peptides. Score 0.394 Round 4: 215 peptides, 32 chains. Longest chain 17 peptides. Score 0.435 Round 5: 214 peptides, 31 chains. Longest chain 13 peptides. Score 0.444 Taking the results from Round 5 Chains 31, Residues 183, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5337 reflections ( 98.03 % complete ) and 8695 restraints for refining 3668 atoms. 7994 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2375 (Rfree = 0.000) for 3668 atoms. Found 7 (17 requested) and removed 14 (8 requested) atoms. Cycle 22: After refmac, R = 0.2129 (Rfree = 0.000) for 3650 atoms. Found 3 (17 requested) and removed 13 (8 requested) atoms. Cycle 23: After refmac, R = 0.2206 (Rfree = 0.000) for 3635 atoms. Found 13 (17 requested) and removed 13 (8 requested) atoms. Cycle 24: After refmac, R = 0.2225 (Rfree = 0.000) for 3629 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 25: After refmac, R = 0.2276 (Rfree = 0.000) for 3613 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.69 3.50 Search for helices and strands: 0 residues in 0 chains, 3672 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3690 seeds are put forward Round 1: 177 peptides, 35 chains. Longest chain 10 peptides. Score 0.289 Round 2: 175 peptides, 29 chains. Longest chain 14 peptides. Score 0.361 Round 3: 171 peptides, 31 chains. Longest chain 10 peptides. Score 0.323 Round 4: 188 peptides, 31 chains. Longest chain 11 peptides. Score 0.373 Round 5: 174 peptides, 29 chains. Longest chain 11 peptides. Score 0.358 Taking the results from Round 4 Chains 31, Residues 157, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5337 reflections ( 98.03 % complete ) and 8659 restraints for refining 3669 atoms. 8062 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2304 (Rfree = 0.000) for 3669 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 27: After refmac, R = 0.2307 (Rfree = 0.000) for 3655 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 28: After refmac, R = 0.2011 (Rfree = 0.000) for 3636 atoms. Found 13 (17 requested) and removed 12 (8 requested) atoms. Cycle 29: After refmac, R = 0.2122 (Rfree = 0.000) for 3623 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 30: After refmac, R = 0.1965 (Rfree = 0.000) for 3617 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.73 3.54 Search for helices and strands: 0 residues in 0 chains, 3707 seeds are put forward NCS extension: 0 residues added, 3707 seeds are put forward Round 1: 142 peptides, 29 chains. Longest chain 9 peptides. Score 0.259 Round 2: 163 peptides, 31 chains. Longest chain 9 peptides. Score 0.299 Round 3: 164 peptides, 30 chains. Longest chain 9 peptides. Score 0.315 Round 4: 166 peptides, 29 chains. Longest chain 10 peptides. Score 0.335 Round 5: 174 peptides, 32 chains. Longest chain 11 peptides. Score 0.319 Taking the results from Round 4 Chains 29, Residues 137, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5337 reflections ( 98.03 % complete ) and 8674 restraints for refining 3670 atoms. 8155 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2129 (Rfree = 0.000) for 3670 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. Cycle 32: After refmac, R = 0.2061 (Rfree = 0.000) for 3654 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. Cycle 33: After refmac, R = 0.1931 (Rfree = 0.000) for 3632 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 34: After refmac, R = 0.1858 (Rfree = 0.000) for 3626 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 35: After refmac, R = 0.1884 (Rfree = 0.000) for 3626 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.69 3.50 Search for helices and strands: 0 residues in 0 chains, 3711 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3723 seeds are put forward Round 1: 149 peptides, 35 chains. Longest chain 6 peptides. Score 0.198 Round 2: 176 peptides, 35 chains. Longest chain 8 peptides. Score 0.286 Round 3: 169 peptides, 32 chains. Longest chain 13 peptides. Score 0.304 Round 4: 172 peptides, 33 chains. Longest chain 14 peptides. Score 0.300 Round 5: 185 peptides, 35 chains. Longest chain 12 peptides. Score 0.313 Taking the results from Round 5 Chains 35, Residues 150, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5337 reflections ( 98.03 % complete ) and 8636 restraints for refining 3670 atoms. 8071 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1898 (Rfree = 0.000) for 3670 atoms. Found 10 (17 requested) and removed 18 (8 requested) atoms. Cycle 37: After refmac, R = 0.1971 (Rfree = 0.000) for 3642 atoms. Found 14 (17 requested) and removed 14 (8 requested) atoms. Cycle 38: After refmac, R = 0.1894 (Rfree = 0.000) for 3633 atoms. Found 11 (17 requested) and removed 12 (8 requested) atoms. Cycle 39: After refmac, R = 0.1857 (Rfree = 0.000) for 3620 atoms. Found 7 (17 requested) and removed 20 (8 requested) atoms. Cycle 40: After refmac, R = 0.1701 (Rfree = 0.000) for 3594 atoms. Found 14 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.64 3.45 Search for helices and strands: 0 residues in 0 chains, 3677 seeds are put forward NCS extension: 0 residues added, 3677 seeds are put forward Round 1: 145 peptides, 32 chains. Longest chain 8 peptides. Score 0.227 Round 2: 157 peptides, 33 chains. Longest chain 6 peptides. Score 0.253 Round 3: 161 peptides, 30 chains. Longest chain 9 peptides. Score 0.306 Round 4: 155 peptides, 31 chains. Longest chain 8 peptides. Score 0.274 Round 5: 168 peptides, 32 chains. Longest chain 10 peptides. Score 0.301 Taking the results from Round 3 Chains 30, Residues 131, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5337 reflections ( 98.03 % complete ) and 8553 restraints for refining 3644 atoms. 8059 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1972 (Rfree = 0.000) for 3644 atoms. Found 14 (17 requested) and removed 22 (8 requested) atoms. Cycle 42: After refmac, R = 0.1913 (Rfree = 0.000) for 3619 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 43: After refmac, R = 0.2038 (Rfree = 0.000) for 3610 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 44: After refmac, R = 0.2028 (Rfree = 0.000) for 3593 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 45: After refmac, R = 0.2202 (Rfree = 0.000) for 3574 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.60 3.41 Search for helices and strands: 0 residues in 0 chains, 3665 seeds are put forward NCS extension: 0 residues added, 3665 seeds are put forward Round 1: 116 peptides, 27 chains. Longest chain 7 peptides. Score 0.197 Round 2: 135 peptides, 29 chains. Longest chain 7 peptides. Score 0.235 Round 3: 132 peptides, 26 chains. Longest chain 10 peptides. Score 0.269 Round 4: 120 peptides, 25 chains. Longest chain 8 peptides. Score 0.242 Round 5: 115 peptides, 24 chains. Longest chain 9 peptides. Score 0.239 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 106, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence Sequence coverage is 14 % Consider running further cycles of model building using 2it9-4_warpNtrace.pdb as input Building loops using Loopy2018 26 chains (106 residues) following loop building 2 chains (15 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5337 reflections ( 98.03 % complete ) and 8039 restraints for refining 3515 atoms. 7586 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1992 (Rfree = 0.000) for 3515 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2028 (Rfree = 0.000) for 3491 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2009 (Rfree = 0.000) for 3468 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2025 (Rfree = 0.000) for 3452 atoms. TimeTaking 55.63