Tue 25 Dec 19:27:57 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 2hi0-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hi0-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hi0-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hi0-3.4-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/2hi0-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hi0-3.4-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 ============================================================ Tue 25 Dec 19:28:06 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/2hi0-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hi0-3.4-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 324 and 0 Target number of residues in the AU: 324 Target solvent content: 0.6232 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: 2hi0-3.4-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: 2hi0-3.4-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 3.401 Wilson plot Bfac: 62.91 6602 reflections ( 99.80 % complete ) and 0 restraints for refining 4230 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3131 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2750 (Rfree = 0.000) for 4230 atoms. Found 31 (31 requested) and removed 43 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.24 3.51 Search for helices and strands: 0 residues in 0 chains, 4327 seeds are put forward NCS extension: 0 residues added, 4327 seeds are put forward Round 1: 229 peptides, 47 chains. Longest chain 10 peptides. Score 0.321 Round 2: 277 peptides, 47 chains. Longest chain 11 peptides. Score 0.480 Round 3: 284 peptides, 44 chains. Longest chain 17 peptides. Score 0.537 Round 4: 290 peptides, 47 chains. Longest chain 12 peptides. Score 0.518 Round 5: 290 peptides, 40 chains. Longest chain 20 peptides. Score 0.600 Taking the results from Round 5 Chains 42, Residues 250, Estimated correctness of the model 28.6 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 6602 reflections ( 99.80 % complete ) and 7509 restraints for refining 3492 atoms. 6479 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2399 (Rfree = 0.000) for 3492 atoms. Found 13 (26 requested) and removed 36 (13 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2191 (Rfree = 0.000) for 3440 atoms. Found 12 (26 requested) and removed 21 (13 requested) atoms. Cycle 3: After refmac, R = 0.2193 (Rfree = 0.000) for 3414 atoms. Found 11 (25 requested) and removed 14 (12 requested) atoms. Cycle 4: After refmac, R = 0.2064 (Rfree = 0.000) for 3401 atoms. Found 11 (25 requested) and removed 16 (12 requested) atoms. Cycle 5: After refmac, R = 0.2009 (Rfree = 0.000) for 3385 atoms. Found 6 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.25 3.52 Search for helices and strands: 0 residues in 0 chains, 3508 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3521 seeds are put forward Round 1: 241 peptides, 49 chains. Longest chain 13 peptides. Score 0.334 Round 2: 257 peptides, 43 chains. Longest chain 18 peptides. Score 0.471 Round 3: 261 peptides, 37 chains. Longest chain 24 peptides. Score 0.558 Round 4: 270 peptides, 40 chains. Longest chain 25 peptides. Score 0.547 Round 5: 257 peptides, 36 chains. Longest chain 23 peptides. Score 0.559 Taking the results from Round 5 Chains 38, Residues 221, Estimated correctness of the model 14.7 % 3 chains (36 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6602 reflections ( 99.80 % complete ) and 7814 restraints for refining 3490 atoms. 6850 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2175 (Rfree = 0.000) for 3490 atoms. Found 22 (26 requested) and removed 33 (13 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2016 (Rfree = 0.000) for 3457 atoms. Found 15 (26 requested) and removed 26 (13 requested) atoms. Cycle 8: After refmac, R = 0.1949 (Rfree = 0.000) for 3441 atoms. Found 16 (25 requested) and removed 19 (12 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.1705 (Rfree = 0.000) for 3438 atoms. Found 4 (25 requested) and removed 17 (12 requested) atoms. Cycle 10: After refmac, R = 0.1758 (Rfree = 0.000) for 3418 atoms. Found 4 (25 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.22 3.49 Search for helices and strands: 0 residues in 0 chains, 3533 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 3549 seeds are put forward Round 1: 231 peptides, 42 chains. Longest chain 11 peptides. Score 0.401 Round 2: 280 peptides, 43 chains. Longest chain 24 peptides. Score 0.538 Round 3: 281 peptides, 40 chains. Longest chain 18 peptides. Score 0.577 Round 4: 276 peptides, 41 chains. Longest chain 17 peptides. Score 0.551 Round 5: 288 peptides, 39 chains. Longest chain 20 peptides. Score 0.606 Taking the results from Round 5 Chains 40, Residues 249, Estimated correctness of the model 30.6 % 3 chains (38 residues) have been docked in sequence ------------------------------------------------------ 6602 reflections ( 99.80 % complete ) and 7507 restraints for refining 3492 atoms. 6407 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2076 (Rfree = 0.000) for 3492 atoms. Found 26 (26 requested) and removed 25 (13 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.1910 (Rfree = 0.000) for 3483 atoms. Found 11 (26 requested) and removed 14 (13 requested) atoms. Cycle 13: After refmac, R = 0.1895 (Rfree = 0.000) for 3471 atoms. Found 15 (26 requested) and removed 20 (13 requested) atoms. Cycle 14: After refmac, R = 0.1847 (Rfree = 0.000) for 3461 atoms. Found 8 (26 requested) and removed 18 (13 requested) atoms. Cycle 15: After refmac, R = 0.1830 (Rfree = 0.000) for 3445 atoms. Found 8 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.22 3.49 Search for helices and strands: 0 residues in 0 chains, 3560 seeds are put forward NCS extension: 29 residues added (4 deleted due to clashes), 3589 seeds are put forward Round 1: 224 peptides, 38 chains. Longest chain 15 peptides. Score 0.434 Round 2: 249 peptides, 35 chains. Longest chain 14 peptides. Score 0.549 Round 3: 259 peptides, 36 chains. Longest chain 17 peptides. Score 0.565 Round 4: 271 peptides, 38 chains. Longest chain 19 peptides. Score 0.573 Round 5: 263 peptides, 38 chains. Longest chain 19 peptides. Score 0.552 Taking the results from Round 4 Chains 38, Residues 233, Estimated correctness of the model 19.5 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 6602 reflections ( 99.80 % complete ) and 7920 restraints for refining 3492 atoms. 7004 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1917 (Rfree = 0.000) for 3492 atoms. Found 21 (26 requested) and removed 15 (13 requested) atoms. Cycle 17: After refmac, R = 0.1827 (Rfree = 0.000) for 3490 atoms. Found 12 (26 requested) and removed 14 (13 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1747 (Rfree = 0.000) for 3481 atoms. Found 9 (26 requested) and removed 16 (13 requested) atoms. Cycle 19: After refmac, R = 0.1729 (Rfree = 0.000) for 3472 atoms. Found 5 (26 requested) and removed 13 (13 requested) atoms. Cycle 20: After refmac, R = 0.1549 (Rfree = 0.000) for 3463 atoms. Found 6 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.26 3.53 Search for helices and strands: 0 residues in 0 chains, 3585 seeds are put forward NCS extension: 31 residues added (0 deleted due to clashes), 3616 seeds are put forward Round 1: 202 peptides, 38 chains. Longest chain 13 peptides. Score 0.359 Round 2: 219 peptides, 34 chains. Longest chain 13 peptides. Score 0.474 Round 3: 227 peptides, 37 chains. Longest chain 14 peptides. Score 0.458 Round 4: 215 peptides, 33 chains. Longest chain 16 peptides. Score 0.475 Round 5: 229 peptides, 33 chains. Longest chain 20 peptides. Score 0.517 Taking the results from Round 5 Chains 35, Residues 196, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6602 reflections ( 99.80 % complete ) and 8050 restraints for refining 3492 atoms. 7224 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1942 (Rfree = 0.000) for 3492 atoms. Found 11 (26 requested) and removed 15 (13 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1869 (Rfree = 0.000) for 3483 atoms. Found 10 (26 requested) and removed 15 (13 requested) atoms. Cycle 23: After refmac, R = 0.1753 (Rfree = 0.000) for 3477 atoms. Found 4 (26 requested) and removed 14 (13 requested) atoms. Cycle 24: After refmac, R = 0.1726 (Rfree = 0.000) for 3463 atoms. Found 3 (26 requested) and removed 13 (13 requested) atoms. Cycle 25: After refmac, R = 0.1676 (Rfree = 0.000) for 3451 atoms. Found 6 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 3.54 Search for helices and strands: 0 residues in 0 chains, 3560 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3578 seeds are put forward Round 1: 208 peptides, 39 chains. Longest chain 12 peptides. Score 0.365 Round 2: 238 peptides, 35 chains. Longest chain 16 peptides. Score 0.518 Round 3: 237 peptides, 32 chains. Longest chain 24 peptides. Score 0.553 Round 4: 222 peptides, 33 chains. Longest chain 20 peptides. Score 0.496 Round 5: 239 peptides, 31 chains. Longest chain 24 peptides. Score 0.571 Taking the results from Round 5 Chains 33, Residues 208, Estimated correctness of the model 18.9 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 6602 reflections ( 99.80 % complete ) and 7795 restraints for refining 3492 atoms. 6900 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1949 (Rfree = 0.000) for 3492 atoms. Found 18 (26 requested) and removed 19 (13 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1827 (Rfree = 0.000) for 3481 atoms. Found 7 (26 requested) and removed 16 (13 requested) atoms. Cycle 28: After refmac, R = 0.1784 (Rfree = 0.000) for 3471 atoms. Found 9 (26 requested) and removed 15 (13 requested) atoms. Cycle 29: After refmac, R = 0.1677 (Rfree = 0.000) for 3462 atoms. Found 10 (26 requested) and removed 13 (13 requested) atoms. Cycle 30: After refmac, R = 0.1595 (Rfree = 0.000) for 3457 atoms. Found 6 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.23 3.50 Search for helices and strands: 0 residues in 0 chains, 3574 seeds are put forward NCS extension: 14 residues added (4 deleted due to clashes), 3588 seeds are put forward Round 1: 201 peptides, 37 chains. Longest chain 11 peptides. Score 0.371 Round 2: 217 peptides, 32 chains. Longest chain 15 peptides. Score 0.495 Round 3: 229 peptides, 33 chains. Longest chain 16 peptides. Score 0.517 Round 4: 210 peptides, 32 chains. Longest chain 14 peptides. Score 0.473 Round 5: 229 peptides, 32 chains. Longest chain 16 peptides. Score 0.530 Taking the results from Round 5 Chains 32, Residues 197, Estimated correctness of the model 4.1 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 6602 reflections ( 99.80 % complete ) and 8070 restraints for refining 3492 atoms. 7263 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1965 (Rfree = 0.000) for 3492 atoms. Found 24 (26 requested) and removed 20 (13 requested) atoms. Cycle 32: After refmac, R = 0.1791 (Rfree = 0.000) for 3487 atoms. Found 15 (26 requested) and removed 14 (13 requested) atoms. Cycle 33: After refmac, R = 0.1663 (Rfree = 0.000) for 3486 atoms. Found 10 (26 requested) and removed 13 (13 requested) atoms. Cycle 34: After refmac, R = 0.1606 (Rfree = 0.000) for 3482 atoms. Found 3 (26 requested) and removed 13 (13 requested) atoms. Cycle 35: After refmac, R = 0.1587 (Rfree = 0.000) for 3471 atoms. Found 6 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.24 3.51 Search for helices and strands: 0 residues in 0 chains, 3574 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3596 seeds are put forward Round 1: 193 peptides, 36 chains. Longest chain 15 peptides. Score 0.357 Round 2: 224 peptides, 37 chains. Longest chain 16 peptides. Score 0.448 Round 3: 230 peptides, 35 chains. Longest chain 16 peptides. Score 0.494 Round 4: 216 peptides, 36 chains. Longest chain 16 peptides. Score 0.436 Round 5: 201 peptides, 32 chains. Longest chain 13 peptides. Score 0.444 Taking the results from Round 3 Chains 35, Residues 195, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 6602 reflections ( 99.80 % complete ) and 7983 restraints for refining 3492 atoms. 7187 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1799 (Rfree = 0.000) for 3492 atoms. Found 18 (26 requested) and removed 13 (13 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.1669 (Rfree = 0.000) for 3489 atoms. Found 4 (26 requested) and removed 13 (13 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1631 (Rfree = 0.000) for 3476 atoms. Found 5 (26 requested) and removed 13 (13 requested) atoms. Cycle 39: After refmac, R = 0.1569 (Rfree = 0.000) for 3467 atoms. Found 5 (26 requested) and removed 13 (13 requested) atoms. Cycle 40: After refmac, R = 0.1570 (Rfree = 0.000) for 3458 atoms. Found 3 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 3.52 Search for helices and strands: 0 residues in 0 chains, 3558 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3576 seeds are put forward Round 1: 170 peptides, 31 chains. Longest chain 13 peptides. Score 0.351 Round 2: 207 peptides, 35 chains. Longest chain 15 peptides. Score 0.421 Round 3: 205 peptides, 32 chains. Longest chain 16 peptides. Score 0.457 Round 4: 211 peptides, 33 chains. Longest chain 17 peptides. Score 0.462 Round 5: 220 peptides, 31 chains. Longest chain 17 peptides. Score 0.517 Taking the results from Round 5 Chains 33, Residues 189, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6602 reflections ( 99.80 % complete ) and 8006 restraints for refining 3491 atoms. 7246 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1824 (Rfree = 0.000) for 3491 atoms. Found 14 (26 requested) and removed 16 (13 requested) atoms. Cycle 42: After refmac, R = 0.1772 (Rfree = 0.000) for 3482 atoms. Found 5 (26 requested) and removed 16 (13 requested) atoms. Cycle 43: After refmac, R = 0.1693 (Rfree = 0.000) for 3471 atoms. Found 20 (26 requested) and removed 13 (13 requested) atoms. Cycle 44: After refmac, R = 0.1575 (Rfree = 0.000) for 3475 atoms. Found 1 (26 requested) and removed 13 (13 requested) atoms. Cycle 45: After refmac, R = 0.1554 (Rfree = 0.000) for 3463 atoms. Found 6 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.24 3.51 Search for helices and strands: 0 residues in 0 chains, 3556 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 3573 seeds are put forward Round 1: 152 peptides, 31 chains. Longest chain 12 peptides. Score 0.283 Round 2: 171 peptides, 29 chains. Longest chain 13 peptides. Score 0.386 Round 3: 165 peptides, 29 chains. Longest chain 17 peptides. Score 0.364 Round 4: 169 peptides, 28 chains. Longest chain 17 peptides. Score 0.394 Round 5: 171 peptides, 28 chains. Longest chain 17 peptides. Score 0.401 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 143, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 2hi0-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6602 reflections ( 99.80 % complete ) and 8207 restraints for refining 3492 atoms. 7621 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1750 (Rfree = 0.000) for 3492 atoms. Found 0 (26 requested) and removed 11 (13 requested) atoms. Cycle 47: After refmac, R = 0.1788 (Rfree = 0.000) for 3480 atoms. Found 0 (26 requested) and removed 3 (13 requested) atoms. Cycle 48: After refmac, R = 0.1698 (Rfree = 0.000) for 3476 atoms. Found 0 (26 requested) and removed 5 (13 requested) atoms. Cycle 49: After refmac, R = 0.1603 (Rfree = 0.000) for 3468 atoms. Found 0 (26 requested) and removed 4 (13 requested) atoms. Writing output files ... TimeTaking 57.51