Sun 23 Dec 22:22:59 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 2hi0-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hi0-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hi0-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hi0-3.6-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/2hi0-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hi0-3.6-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 22:23:08 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/2hi0-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hi0-3.6-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 313 and 0 Target number of residues in the AU: 313 Target solvent content: 0.6360 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: 2hi0-3.6-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: 2hi0-3.6-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 3.600 Wilson plot Bfac: 69.72 5572 reflections ( 99.77 % complete ) and 0 restraints for refining 4238 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3214 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2893 (Rfree = 0.000) for 4238 atoms. Found 24 (27 requested) and removed 34 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.40 3.68 Search for helices and strands: 0 residues in 0 chains, 4341 seeds are put forward NCS extension: 0 residues added, 4341 seeds are put forward Round 1: 168 peptides, 34 chains. Longest chain 7 peptides. Score 0.296 Round 2: 216 peptides, 41 chains. Longest chain 11 peptides. Score 0.364 Round 3: 227 peptides, 36 chains. Longest chain 14 peptides. Score 0.471 Round 4: 239 peptides, 34 chains. Longest chain 17 peptides. Score 0.534 Round 5: 244 peptides, 35 chains. Longest chain 11 peptides. Score 0.535 Taking the results from Round 5 Chains 35, Residues 209, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5572 reflections ( 99.77 % complete ) and 8103 restraints for refining 3480 atoms. 7302 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2534 (Rfree = 0.000) for 3480 atoms. Found 15 (22 requested) and removed 21 (11 requested) atoms. Cycle 2: After refmac, R = 0.2307 (Rfree = 0.000) for 3418 atoms. Found 9 (22 requested) and removed 20 (11 requested) atoms. Cycle 3: After refmac, R = 0.2096 (Rfree = 0.000) for 3386 atoms. Found 12 (21 requested) and removed 16 (10 requested) atoms. Cycle 4: After refmac, R = 0.2073 (Rfree = 0.000) for 3365 atoms. Found 21 (21 requested) and removed 14 (10 requested) atoms. Cycle 5: After refmac, R = 0.1839 (Rfree = 0.000) for 3360 atoms. Found 13 (21 requested) and removed 19 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.39 3.67 Search for helices and strands: 0 residues in 0 chains, 3514 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 3524 seeds are put forward Round 1: 208 peptides, 41 chains. Longest chain 10 peptides. Score 0.336 Round 2: 240 peptides, 41 chains. Longest chain 14 peptides. Score 0.444 Round 3: 233 peptides, 40 chains. Longest chain 10 peptides. Score 0.436 Round 4: 248 peptides, 41 chains. Longest chain 12 peptides. Score 0.470 Round 5: 248 peptides, 40 chains. Longest chain 14 peptides. Score 0.483 Taking the results from Round 5 Chains 40, Residues 208, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5572 reflections ( 99.77 % complete ) and 7980 restraints for refining 3447 atoms. 7188 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2008 (Rfree = 0.000) for 3447 atoms. Found 16 (22 requested) and removed 19 (11 requested) atoms. Cycle 7: After refmac, R = 0.1771 (Rfree = 0.000) for 3427 atoms. Found 10 (22 requested) and removed 13 (11 requested) atoms. Cycle 8: After refmac, R = 0.1738 (Rfree = 0.000) for 3409 atoms. Found 12 (21 requested) and removed 19 (10 requested) atoms. Cycle 9: After refmac, R = 0.1624 (Rfree = 0.000) for 3393 atoms. Found 12 (21 requested) and removed 14 (10 requested) atoms. Cycle 10: After refmac, R = 0.1610 (Rfree = 0.000) for 3383 atoms. Found 9 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.41 3.70 Search for helices and strands: 0 residues in 0 chains, 3520 seeds are put forward NCS extension: 18 residues added (4 deleted due to clashes), 3538 seeds are put forward Round 1: 210 peptides, 39 chains. Longest chain 11 peptides. Score 0.372 Round 2: 233 peptides, 37 chains. Longest chain 14 peptides. Score 0.477 Round 3: 240 peptides, 39 chains. Longest chain 13 peptides. Score 0.471 Round 4: 235 peptides, 35 chains. Longest chain 12 peptides. Score 0.509 Round 5: 238 peptides, 34 chains. Longest chain 16 peptides. Score 0.531 Taking the results from Round 5 Chains 35, Residues 204, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 5572 reflections ( 99.77 % complete ) and 7933 restraints for refining 3481 atoms. 7093 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1951 (Rfree = 0.000) for 3481 atoms. Found 9 (22 requested) and removed 13 (11 requested) atoms. Cycle 12: After refmac, R = 0.1724 (Rfree = 0.000) for 3458 atoms. Found 4 (22 requested) and removed 17 (11 requested) atoms. Cycle 13: After refmac, R = 0.1639 (Rfree = 0.000) for 3439 atoms. Found 1 (22 requested) and removed 11 (11 requested) atoms. Cycle 14: After refmac, R = 0.1612 (Rfree = 0.000) for 3424 atoms. Found 2 (21 requested) and removed 13 (10 requested) atoms. Cycle 15: After refmac, R = 0.1604 (Rfree = 0.000) for 3413 atoms. Found 2 (21 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.41 3.70 Search for helices and strands: 0 residues in 0 chains, 3513 seeds are put forward NCS extension: 0 residues added, 3513 seeds are put forward Round 1: 185 peptides, 34 chains. Longest chain 12 peptides. Score 0.359 Round 2: 222 peptides, 34 chains. Longest chain 17 peptides. Score 0.483 Round 3: 239 peptides, 33 chains. Longest chain 18 peptides. Score 0.546 Round 4: 225 peptides, 35 chains. Longest chain 16 peptides. Score 0.479 Round 5: 233 peptides, 37 chains. Longest chain 12 peptides. Score 0.477 Taking the results from Round 3 Chains 34, Residues 206, Estimated correctness of the model 0.0 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 5572 reflections ( 99.77 % complete ) and 7770 restraints for refining 3480 atoms. 6876 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1952 (Rfree = 0.000) for 3480 atoms. Found 20 (22 requested) and removed 22 (11 requested) atoms. Cycle 17: After refmac, R = 0.1766 (Rfree = 0.000) for 3472 atoms. Found 10 (22 requested) and removed 14 (11 requested) atoms. Cycle 18: After refmac, R = 0.1718 (Rfree = 0.000) for 3463 atoms. Found 7 (22 requested) and removed 12 (11 requested) atoms. Cycle 19: After refmac, R = 0.1677 (Rfree = 0.000) for 3451 atoms. Found 12 (22 requested) and removed 13 (11 requested) atoms. Cycle 20: After refmac, R = 0.1651 (Rfree = 0.000) for 3445 atoms. Found 14 (22 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.65 Search for helices and strands: 0 residues in 0 chains, 3560 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 3583 seeds are put forward Round 1: 217 peptides, 46 chains. Longest chain 10 peptides. Score 0.293 Round 2: 226 peptides, 39 chains. Longest chain 11 peptides. Score 0.427 Round 3: 226 peptides, 39 chains. Longest chain 10 peptides. Score 0.427 Round 4: 228 peptides, 37 chains. Longest chain 10 peptides. Score 0.461 Round 5: 233 peptides, 40 chains. Longest chain 13 peptides. Score 0.436 Taking the results from Round 4 Chains 37, Residues 191, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5572 reflections ( 99.77 % complete ) and 8137 restraints for refining 3481 atoms. 7410 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1955 (Rfree = 0.000) for 3481 atoms. Found 15 (22 requested) and removed 13 (11 requested) atoms. Cycle 22: After refmac, R = 0.1817 (Rfree = 0.000) for 3471 atoms. Found 11 (22 requested) and removed 12 (11 requested) atoms. Cycle 23: After refmac, R = 0.1694 (Rfree = 0.000) for 3464 atoms. Found 13 (22 requested) and removed 15 (11 requested) atoms. Cycle 24: After refmac, R = 0.1730 (Rfree = 0.000) for 3459 atoms. Found 12 (22 requested) and removed 13 (11 requested) atoms. Cycle 25: After refmac, R = 0.1546 (Rfree = 0.000) for 3456 atoms. Found 13 (22 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.38 3.66 Search for helices and strands: 0 residues in 0 chains, 3579 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3591 seeds are put forward Round 1: 176 peptides, 37 chains. Longest chain 7 peptides. Score 0.279 Round 2: 211 peptides, 37 chains. Longest chain 11 peptides. Score 0.405 Round 3: 216 peptides, 35 chains. Longest chain 11 peptides. Score 0.450 Round 4: 207 peptides, 35 chains. Longest chain 12 peptides. Score 0.421 Round 5: 212 peptides, 36 chains. Longest chain 11 peptides. Score 0.423 Taking the results from Round 3 Chains 35, Residues 181, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5572 reflections ( 99.77 % complete ) and 8244 restraints for refining 3481 atoms. 7555 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1882 (Rfree = 0.000) for 3481 atoms. Found 20 (22 requested) and removed 14 (11 requested) atoms. Cycle 27: After refmac, R = 0.1736 (Rfree = 0.000) for 3465 atoms. Found 20 (22 requested) and removed 11 (11 requested) atoms. Cycle 28: After refmac, R = 0.1588 (Rfree = 0.000) for 3460 atoms. Found 13 (22 requested) and removed 12 (11 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1632 (Rfree = 0.000) for 3461 atoms. Found 15 (22 requested) and removed 14 (11 requested) atoms. Cycle 30: After refmac, R = 0.1505 (Rfree = 0.000) for 3455 atoms. Found 15 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.66 Search for helices and strands: 0 residues in 0 chains, 3583 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3597 seeds are put forward Round 1: 152 peptides, 31 chains. Longest chain 8 peptides. Score 0.283 Round 2: 188 peptides, 33 chains. Longest chain 12 peptides. Score 0.385 Round 3: 182 peptides, 33 chains. Longest chain 11 peptides. Score 0.364 Round 4: 193 peptides, 32 chains. Longest chain 13 peptides. Score 0.417 Round 5: 177 peptides, 33 chains. Longest chain 11 peptides. Score 0.346 Taking the results from Round 4 Chains 32, Residues 161, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5572 reflections ( 99.77 % complete ) and 8236 restraints for refining 3481 atoms. 7624 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1680 (Rfree = 0.000) for 3481 atoms. Found 16 (22 requested) and removed 13 (11 requested) atoms. Cycle 32: After refmac, R = 0.1555 (Rfree = 0.000) for 3479 atoms. Found 22 (22 requested) and removed 11 (11 requested) atoms. Cycle 33: After refmac, R = 0.1535 (Rfree = 0.000) for 3486 atoms. Found 18 (22 requested) and removed 14 (11 requested) atoms. Cycle 34: After refmac, R = 0.1383 (Rfree = 0.000) for 3487 atoms. Found 11 (22 requested) and removed 12 (11 requested) atoms. Cycle 35: After refmac, R = 0.1429 (Rfree = 0.000) for 3485 atoms. Found 21 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.35 3.63 Search for helices and strands: 0 residues in 0 chains, 3596 seeds are put forward NCS extension: 0 residues added, 3596 seeds are put forward Round 1: 168 peptides, 36 chains. Longest chain 7 peptides. Score 0.264 Round 2: 198 peptides, 40 chains. Longest chain 9 peptides. Score 0.314 Round 3: 180 peptides, 32 chains. Longest chain 14 peptides. Score 0.372 Round 4: 159 peptides, 28 chains. Longest chain 10 peptides. Score 0.358 Round 5: 171 peptides, 27 chains. Longest chain 13 peptides. Score 0.417 Taking the results from Round 5 Chains 27, Residues 144, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5572 reflections ( 99.77 % complete ) and 8329 restraints for refining 3481 atoms. 7761 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1890 (Rfree = 0.000) for 3481 atoms. Found 22 (22 requested) and removed 14 (11 requested) atoms. Cycle 37: After refmac, R = 0.1661 (Rfree = 0.000) for 3477 atoms. Found 22 (22 requested) and removed 12 (11 requested) atoms. Cycle 38: After refmac, R = 0.1642 (Rfree = 0.000) for 3477 atoms. Found 22 (22 requested) and removed 12 (11 requested) atoms. Cycle 39: After refmac, R = 0.1471 (Rfree = 0.000) for 3482 atoms. Found 20 (22 requested) and removed 12 (11 requested) atoms. Cycle 40: After refmac, R = 0.1410 (Rfree = 0.000) for 3486 atoms. Found 13 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.36 3.64 Search for helices and strands: 0 residues in 0 chains, 3583 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3598 seeds are put forward Round 1: 137 peptides, 31 chains. Longest chain 8 peptides. Score 0.222 Round 2: 160 peptides, 33 chains. Longest chain 8 peptides. Score 0.282 Round 3: 182 peptides, 35 chains. Longest chain 9 peptides. Score 0.333 Round 4: 175 peptides, 32 chains. Longest chain 13 peptides. Score 0.354 Round 5: 171 peptides, 33 chains. Longest chain 11 peptides. Score 0.323 Taking the results from Round 4 Chains 32, Residues 143, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 5572 reflections ( 99.77 % complete ) and 8203 restraints for refining 3481 atoms. 7617 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1579 (Rfree = 0.000) for 3481 atoms. Found 21 (22 requested) and removed 13 (11 requested) atoms. Cycle 42: After refmac, R = 0.1599 (Rfree = 0.000) for 3476 atoms. Found 22 (22 requested) and removed 14 (11 requested) atoms. Cycle 43: After refmac, R = 0.1437 (Rfree = 0.000) for 3470 atoms. Found 21 (22 requested) and removed 13 (11 requested) atoms. Cycle 44: After refmac, R = 0.1495 (Rfree = 0.000) for 3472 atoms. Found 20 (22 requested) and removed 11 (11 requested) atoms. Cycle 45: After refmac, R = 0.1346 (Rfree = 0.000) for 3478 atoms. Found 15 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.40 3.68 Search for helices and strands: 0 residues in 0 chains, 3602 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3620 seeds are put forward Round 1: 133 peptides, 30 chains. Longest chain 8 peptides. Score 0.223 Round 2: 145 peptides, 27 chains. Longest chain 11 peptides. Score 0.322 Round 3: 150 peptides, 28 chains. Longest chain 15 peptides. Score 0.325 Round 4: 151 peptides, 28 chains. Longest chain 13 peptides. Score 0.329 Round 5: 149 peptides, 27 chains. Longest chain 13 peptides. Score 0.337 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 122, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2hi0-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5572 reflections ( 99.77 % complete ) and 8344 restraints for refining 3481 atoms. 7847 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1590 (Rfree = 0.000) for 3481 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.1551 (Rfree = 0.000) for 3461 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.1386 (Rfree = 0.000) for 3448 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1378 (Rfree = 0.000) for 3433 atoms. TimeTaking 53.78