Sun 23 Dec 22:22:53 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 2hi0-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hi0-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hi0-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hi0-3.8-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/2hi0-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hi0-3.8-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 22:23:03 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/2hi0-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hi0-3.8-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 301 and 0 Target number of residues in the AU: 301 Target solvent content: 0.6499 Checking the provided sequence file Detected sequence length: 240 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 480 Adjusted target solvent content: 0.44 Input MTZ file: 2hi0-3.8-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: 58.636 38.695 103.583 90.000 98.094 90.000 Input sequence file: 2hi0-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 3840 target number of atoms Had to go as low as 0.65 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: 102.551 3.800 Wilson plot Bfac: 78.00 4764 reflections ( 99.75 % complete ) and 0 restraints for refining 4256 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3297 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3095 (Rfree = 0.000) for 4256 atoms. Found 23 (23 requested) and removed 24 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 3.88 Search for helices and strands: 0 residues in 0 chains, 4350 seeds are put forward NCS extension: 0 residues added, 4350 seeds are put forward Round 1: 146 peptides, 33 chains. Longest chain 7 peptides. Score 0.226 Round 2: 191 peptides, 37 chains. Longest chain 10 peptides. Score 0.335 Round 3: 197 peptides, 34 chains. Longest chain 12 peptides. Score 0.401 Round 4: 204 peptides, 35 chains. Longest chain 10 peptides. Score 0.411 Round 5: 213 peptides, 34 chains. Longest chain 10 peptides. Score 0.455 Taking the results from Round 5 Chains 34, Residues 179, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4764 reflections ( 99.75 % complete ) and 8209 restraints for refining 3474 atoms. 7508 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2590 (Rfree = 0.000) for 3474 atoms. Found 6 (19 requested) and removed 20 (9 requested) atoms. Cycle 2: After refmac, R = 0.2335 (Rfree = 0.000) for 3405 atoms. Found 6 (19 requested) and removed 12 (9 requested) atoms. Cycle 3: After refmac, R = 0.2260 (Rfree = 0.000) for 3372 atoms. Found 8 (18 requested) and removed 17 (9 requested) atoms. Cycle 4: After refmac, R = 0.2093 (Rfree = 0.000) for 3344 atoms. Found 8 (18 requested) and removed 13 (9 requested) atoms. Cycle 5: After refmac, R = 0.1984 (Rfree = 0.000) for 3326 atoms. Found 6 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.69 4.00 Search for helices and strands: 0 residues in 0 chains, 3449 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 3459 seeds are put forward Round 1: 163 peptides, 34 chains. Longest chain 9 peptides. Score 0.277 Round 2: 218 peptides, 42 chains. Longest chain 11 peptides. Score 0.356 Round 3: 210 peptides, 33 chains. Longest chain 12 peptides. Score 0.459 Round 4: 221 peptides, 38 chains. Longest chain 12 peptides. Score 0.424 Round 5: 217 peptides, 30 chains. Longest chain 14 peptides. Score 0.521 Taking the results from Round 5 Chains 30, Residues 187, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4764 reflections ( 99.75 % complete ) and 7581 restraints for refining 3260 atoms. 6863 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2195 (Rfree = 0.000) for 3260 atoms. Found 16 (17 requested) and removed 30 (8 requested) atoms. Cycle 7: After refmac, R = 0.1982 (Rfree = 0.000) for 3231 atoms. Found 9 (17 requested) and removed 12 (8 requested) atoms. Cycle 8: After refmac, R = 0.1985 (Rfree = 0.000) for 3216 atoms. Found 10 (17 requested) and removed 8 (8 requested) atoms. Cycle 9: After refmac, R = 0.1976 (Rfree = 0.000) for 3212 atoms. Found 8 (17 requested) and removed 10 (8 requested) atoms. Cycle 10: After refmac, R = 0.1798 (Rfree = 0.000) for 3204 atoms. Found 4 (17 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.65 3.96 Search for helices and strands: 0 residues in 0 chains, 3352 seeds are put forward NCS extension: 12 residues added (4 deleted due to clashes), 3364 seeds are put forward Round 1: 191 peptides, 39 chains. Longest chain 10 peptides. Score 0.304 Round 2: 221 peptides, 37 chains. Longest chain 13 peptides. Score 0.438 Round 3: 202 peptides, 35 chains. Longest chain 10 peptides. Score 0.404 Round 4: 212 peptides, 34 chains. Longest chain 14 peptides. Score 0.451 Round 5: 222 peptides, 32 chains. Longest chain 22 peptides. Score 0.510 Taking the results from Round 5 Chains 34, Residues 190, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4764 reflections ( 99.75 % complete ) and 7535 restraints for refining 3331 atoms. 6777 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2407 (Rfree = 0.000) for 3331 atoms. Found 18 (18 requested) and removed 25 (9 requested) atoms. Cycle 12: After refmac, R = 0.1965 (Rfree = 0.000) for 3313 atoms. Found 13 (18 requested) and removed 20 (9 requested) atoms. Cycle 13: After refmac, R = 0.1766 (Rfree = 0.000) for 3302 atoms. Found 6 (18 requested) and removed 16 (9 requested) atoms. Cycle 14: After refmac, R = 0.1683 (Rfree = 0.000) for 3287 atoms. Found 5 (18 requested) and removed 10 (9 requested) atoms. Cycle 15: After refmac, R = 0.1640 (Rfree = 0.000) for 3280 atoms. Found 3 (18 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 3.87 Search for helices and strands: 0 residues in 0 chains, 3397 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 3410 seeds are put forward Round 1: 170 peptides, 37 chains. Longest chain 7 peptides. Score 0.256 Round 2: 193 peptides, 34 chains. Longest chain 17 peptides. Score 0.388 Round 3: 210 peptides, 33 chains. Longest chain 20 peptides. Score 0.459 Round 4: 201 peptides, 34 chains. Longest chain 18 peptides. Score 0.415 Round 5: 196 peptides, 31 chains. Longest chain 12 peptides. Score 0.442 Taking the results from Round 3 Chains 34, Residues 177, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4764 reflections ( 99.75 % complete ) and 7829 restraints for refining 3428 atoms. 7113 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2193 (Rfree = 0.000) for 3428 atoms. Found 18 (18 requested) and removed 33 (9 requested) atoms. Cycle 17: After refmac, R = 0.1924 (Rfree = 0.000) for 3388 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. Cycle 18: After refmac, R = 0.1759 (Rfree = 0.000) for 3375 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 19: After refmac, R = 0.1277 (Rfree = 0.000) for 3366 atoms. Found 6 (18 requested) and removed 14 (9 requested) atoms. Cycle 20: After refmac, R = 0.1178 (Rfree = 0.000) for 3353 atoms. Found 2 (18 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.58 3.88 Search for helices and strands: 0 residues in 0 chains, 3478 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 3495 seeds are put forward Round 1: 189 peptides, 40 chains. Longest chain 9 peptides. Score 0.281 Round 2: 209 peptides, 40 chains. Longest chain 10 peptides. Score 0.354 Round 3: 210 peptides, 37 chains. Longest chain 12 peptides. Score 0.402 Round 4: 221 peptides, 37 chains. Longest chain 17 peptides. Score 0.438 Round 5: 224 peptides, 36 chains. Longest chain 18 peptides. Score 0.462 Taking the results from Round 5 Chains 36, Residues 188, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4764 reflections ( 99.75 % complete ) and 8096 restraints for refining 3474 atoms. 7380 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1883 (Rfree = 0.000) for 3474 atoms. Found 19 (19 requested) and removed 43 (9 requested) atoms. Cycle 22: After refmac, R = 0.1828 (Rfree = 0.000) for 3430 atoms. Found 18 (18 requested) and removed 25 (9 requested) atoms. Cycle 23: After refmac, R = 0.1706 (Rfree = 0.000) for 3405 atoms. Found 15 (18 requested) and removed 23 (9 requested) atoms. Cycle 24: After refmac, R = 0.1318 (Rfree = 0.000) for 3387 atoms. Found 3 (18 requested) and removed 17 (9 requested) atoms. Cycle 25: After refmac, R = 0.1218 (Rfree = 0.000) for 3370 atoms. Found 3 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.57 3.87 Search for helices and strands: 0 residues in 0 chains, 3473 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 3499 seeds are put forward Round 1: 151 peptides, 34 chains. Longest chain 8 peptides. Score 0.229 Round 2: 183 peptides, 35 chains. Longest chain 9 peptides. Score 0.337 Round 3: 187 peptides, 33 chains. Longest chain 14 peptides. Score 0.382 Round 4: 198 peptides, 34 chains. Longest chain 15 peptides. Score 0.405 Round 5: 202 peptides, 35 chains. Longest chain 13 peptides. Score 0.404 Taking the results from Round 4 Chains 34, Residues 164, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4764 reflections ( 99.75 % complete ) and 8175 restraints for refining 3471 atoms. 7553 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1677 (Rfree = 0.000) for 3471 atoms. Found 17 (19 requested) and removed 23 (9 requested) atoms. Cycle 27: After refmac, R = 0.1714 (Rfree = 0.000) for 3454 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 28: After refmac, R = 0.1523 (Rfree = 0.000) for 3449 atoms. Found 17 (19 requested) and removed 17 (9 requested) atoms. Cycle 29: After refmac, R = 0.1594 (Rfree = 0.000) for 3445 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 30: After refmac, R = 0.1495 (Rfree = 0.000) for 3442 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.56 3.86 Search for helices and strands: 0 residues in 0 chains, 3575 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3597 seeds are put forward Round 1: 168 peptides, 36 chains. Longest chain 9 peptides. Score 0.264 Round 2: 200 peptides, 37 chains. Longest chain 13 peptides. Score 0.367 Round 3: 201 peptides, 35 chains. Longest chain 13 peptides. Score 0.400 Round 4: 206 peptides, 34 chains. Longest chain 15 peptides. Score 0.432 Round 5: 205 peptides, 34 chains. Longest chain 13 peptides. Score 0.428 Taking the results from Round 4 Chains 35, Residues 172, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 4764 reflections ( 99.75 % complete ) and 7909 restraints for refining 3474 atoms. 7200 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1627 (Rfree = 0.000) for 3474 atoms. Found 11 (19 requested) and removed 15 (9 requested) atoms. Cycle 32: After refmac, R = 0.1710 (Rfree = 0.000) for 3460 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 33: After refmac, R = 0.1656 (Rfree = 0.000) for 3456 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 34: After refmac, R = 0.1509 (Rfree = 0.000) for 3449 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 35: After refmac, R = 0.1465 (Rfree = 0.000) for 3448 atoms. Found 19 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.55 3.85 Search for helices and strands: 0 residues in 0 chains, 3554 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 3569 seeds are put forward Round 1: 170 peptides, 35 chains. Longest chain 13 peptides. Score 0.288 Round 2: 175 peptides, 33 chains. Longest chain 11 peptides. Score 0.338 Round 3: 194 peptides, 33 chains. Longest chain 12 peptides. Score 0.406 Round 4: 191 peptides, 30 chains. Longest chain 22 peptides. Score 0.440 Round 5: 184 peptides, 29 chains. Longest chain 15 peptides. Score 0.431 Taking the results from Round 4 Chains 31, Residues 161, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4764 reflections ( 99.75 % complete ) and 8139 restraints for refining 3474 atoms. 7490 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1747 (Rfree = 0.000) for 3474 atoms. Found 10 (19 requested) and removed 20 (9 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.1814 (Rfree = 0.000) for 3453 atoms. Found 17 (19 requested) and removed 16 (9 requested) atoms. Cycle 38: After refmac, R = 0.1729 (Rfree = 0.000) for 3448 atoms. Found 18 (18 requested) and removed 10 (9 requested) atoms. Cycle 39: After refmac, R = 0.1556 (Rfree = 0.000) for 3449 atoms. Found 14 (19 requested) and removed 15 (9 requested) atoms. Cycle 40: After refmac, R = 0.1733 (Rfree = 0.000) for 3445 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.54 3.84 Search for helices and strands: 0 residues in 0 chains, 3533 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3548 seeds are put forward Round 1: 161 peptides, 36 chains. Longest chain 12 peptides. Score 0.237 Round 2: 164 peptides, 32 chains. Longest chain 12 peptides. Score 0.313 Round 3: 151 peptides, 31 chains. Longest chain 9 peptides. Score 0.279 Round 4: 170 peptides, 30 chains. Longest chain 13 peptides. Score 0.367 Round 5: 182 peptides, 30 chains. Longest chain 14 peptides. Score 0.409 Taking the results from Round 5 Chains 30, Residues 152, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4764 reflections ( 99.75 % complete ) and 8194 restraints for refining 3472 atoms. 7616 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1861 (Rfree = 0.000) for 3472 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Cycle 42: After refmac, R = 0.1579 (Rfree = 0.000) for 3460 atoms. Found 17 (19 requested) and removed 14 (9 requested) atoms. Cycle 43: After refmac, R = 0.1691 (Rfree = 0.000) for 3455 atoms. Found 14 (19 requested) and removed 17 (9 requested) atoms. Cycle 44: After refmac, R = 0.1648 (Rfree = 0.000) for 3448 atoms. Found 13 (18 requested) and removed 17 (9 requested) atoms. Cycle 45: After refmac, R = 0.1219 (Rfree = 0.000) for 3438 atoms. Found 3 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 3.84 Search for helices and strands: 0 residues in 0 chains, 3528 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 3544 seeds are put forward Round 1: 104 peptides, 22 chains. Longest chain 8 peptides. Score 0.241 Round 2: 130 peptides, 25 chains. Longest chain 10 peptides. Score 0.297 Round 3: 130 peptides, 25 chains. Longest chain 11 peptides. Score 0.297 Round 4: 128 peptides, 24 chains. Longest chain 11 peptides. Score 0.306 Round 5: 141 peptides, 26 chains. Longest chain 13 peptides. Score 0.323 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 115, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2hi0-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4764 reflections ( 99.75 % complete ) and 7983 restraints for refining 3437 atoms. 7523 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1599 (Rfree = 0.000) for 3437 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1850 (Rfree = 0.000) for 3421 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1669 (Rfree = 0.000) for 3407 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1462 (Rfree = 0.000) for 3394 atoms. TimeTaking 52.42