Mon 24 Dec 00:14:15 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2hr2-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2hr2-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2hr2-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hr2-3.4-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2hr2-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hr2-3.4-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 00:14:19 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/mrncs/ArpWArp/wArpResults/WorkingDir/2hr2-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hr2-3.4-parrot-mrncs/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 943 and 0 Target number of residues in the AU: 943 Target solvent content: 0.6438 Checking the provided sequence file Detected sequence length: 159 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 954 Adjusted target solvent content: 0.64 Input MTZ file: 2hr2-3.4-parrot-mrncs.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: 89.090 91.280 176.170 90.000 90.000 90.000 Input sequence file: 2hr2-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 7632 target number of atoms Had to go as low as 0.80 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: 88.085 3.400 Wilson plot Bfac: 74.08 20082 reflections ( 98.41 % complete ) and 0 restraints for refining 8438 atoms. Observations/parameters ratio is 0.59 ------------------------------------------------------ Starting model: R = 0.3145 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2733 (Rfree = 0.000) for 8438 atoms. Found 63 (63 requested) and removed 47 (31 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.36 2.77 Search for helices and strands: 0 residues in 0 chains, 8676 seeds are put forward NCS extension: 0 residues added, 8676 seeds are put forward Round 1: 556 peptides, 90 chains. Longest chain 18 peptides. Score 0.416 Round 2: 658 peptides, 84 chains. Longest chain 23 peptides. Score 0.548 Round 3: 670 peptides, 70 chains. Longest chain 26 peptides. Score 0.615 Round 4: 669 peptides, 70 chains. Longest chain 37 peptides. Score 0.614 Round 5: 669 peptides, 68 chains. Longest chain 33 peptides. Score 0.622 Taking the results from Round 5 Chains 77, Residues 601, Estimated correctness of the model 35.7 % 16 chains (180 residues) have been docked in sequence ------------------------------------------------------ 20082 reflections ( 98.41 % complete ) and 12849 restraints for refining 6937 atoms. 9852 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2600 (Rfree = 0.000) for 6937 atoms. Found 52 (52 requested) and removed 49 (26 requested) atoms. Cycle 2: After refmac, R = 0.2390 (Rfree = 0.000) for 6841 atoms. Found 30 (52 requested) and removed 40 (26 requested) atoms. Cycle 3: After refmac, R = 0.2268 (Rfree = 0.000) for 6789 atoms. Found 20 (51 requested) and removed 34 (25 requested) atoms. Cycle 4: After refmac, R = 0.2180 (Rfree = 0.000) for 6745 atoms. Found 21 (51 requested) and removed 28 (25 requested) atoms. Cycle 5: After refmac, R = 0.2121 (Rfree = 0.000) for 6720 atoms. Found 18 (50 requested) and removed 27 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.39 2.80 Search for helices and strands: 0 residues in 0 chains, 7087 seeds are put forward NCS extension: 43 residues added (2 deleted due to clashes), 7130 seeds are put forward Round 1: 613 peptides, 78 chains. Longest chain 19 peptides. Score 0.531 Round 2: 624 peptides, 68 chains. Longest chain 30 peptides. Score 0.584 Round 3: 636 peptides, 71 chains. Longest chain 23 peptides. Score 0.582 Round 4: 631 peptides, 69 chains. Longest chain 24 peptides. Score 0.586 Round 5: 626 peptides, 68 chains. Longest chain 24 peptides. Score 0.585 Taking the results from Round 4 Chains 78, Residues 562, Estimated correctness of the model 24.0 % 13 chains (137 residues) have been docked in sequence ------------------------------------------------------ 20082 reflections ( 98.41 % complete ) and 13622 restraints for refining 6938 atoms. 10936 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2540 (Rfree = 0.000) for 6938 atoms. Found 52 (52 requested) and removed 41 (26 requested) atoms. Cycle 7: After refmac, R = 0.2323 (Rfree = 0.000) for 6883 atoms. Found 32 (52 requested) and removed 39 (26 requested) atoms. Cycle 8: After refmac, R = 0.2224 (Rfree = 0.000) for 6845 atoms. Found 30 (51 requested) and removed 30 (25 requested) atoms. Cycle 9: After refmac, R = 0.2170 (Rfree = 0.000) for 6836 atoms. Found 21 (51 requested) and removed 27 (25 requested) atoms. Cycle 10: After refmac, R = 0.2131 (Rfree = 0.000) for 6820 atoms. Found 11 (51 requested) and removed 30 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.34 2.76 Search for helices and strands: 0 residues in 0 chains, 7165 seeds are put forward NCS extension: 11 residues added (3 deleted due to clashes), 7176 seeds are put forward Round 1: 582 peptides, 91 chains. Longest chain 16 peptides. Score 0.440 Round 2: 615 peptides, 73 chains. Longest chain 22 peptides. Score 0.554 Round 3: 618 peptides, 72 chains. Longest chain 25 peptides. Score 0.561 Round 4: 599 peptides, 72 chains. Longest chain 22 peptides. Score 0.544 Round 5: 623 peptides, 75 chains. Longest chain 29 peptides. Score 0.553 Taking the results from Round 3 Chains 74, Residues 546, Estimated correctness of the model 15.4 % 10 chains (104 residues) have been docked in sequence ------------------------------------------------------ 20082 reflections ( 98.41 % complete ) and 13931 restraints for refining 6937 atoms. 11474 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2454 (Rfree = 0.000) for 6937 atoms. Found 52 (52 requested) and removed 49 (26 requested) atoms. Cycle 12: After refmac, R = 0.2255 (Rfree = 0.000) for 6902 atoms. Found 30 (52 requested) and removed 36 (26 requested) atoms. Cycle 13: After refmac, R = 0.2204 (Rfree = 0.000) for 6878 atoms. Found 23 (52 requested) and removed 42 (26 requested) atoms. Cycle 14: After refmac, R = 0.2108 (Rfree = 0.000) for 6844 atoms. Found 17 (51 requested) and removed 28 (25 requested) atoms. Cycle 15: After refmac, R = 0.2046 (Rfree = 0.000) for 6825 atoms. Found 11 (51 requested) and removed 26 (25 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.37 2.78 Search for helices and strands: 0 residues in 0 chains, 7185 seeds are put forward NCS extension: 35 residues added (2 deleted due to clashes), 7220 seeds are put forward Round 1: 562 peptides, 77 chains. Longest chain 26 peptides. Score 0.485 Round 2: 598 peptides, 72 chains. Longest chain 20 peptides. Score 0.543 Round 3: 618 peptides, 74 chains. Longest chain 19 peptides. Score 0.553 Round 4: 636 peptides, 73 chains. Longest chain 25 peptides. Score 0.573 Round 5: 606 peptides, 77 chains. Longest chain 17 peptides. Score 0.529 Taking the results from Round 4 Chains 78, Residues 563, Estimated correctness of the model 19.6 % 10 chains (86 residues) have been docked in sequence ------------------------------------------------------ 20082 reflections ( 98.41 % complete ) and 13970 restraints for refining 6938 atoms. 11504 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2512 (Rfree = 0.000) for 6938 atoms. Found 52 (52 requested) and removed 50 (26 requested) atoms. Cycle 17: After refmac, R = 0.2228 (Rfree = 0.000) for 6894 atoms. Found 26 (52 requested) and removed 35 (26 requested) atoms. Cycle 18: After refmac, R = 0.2133 (Rfree = 0.000) for 6859 atoms. Found 13 (51 requested) and removed 31 (25 requested) atoms. Cycle 19: After refmac, R = 0.2072 (Rfree = 0.000) for 6821 atoms. Found 7 (51 requested) and removed 28 (25 requested) atoms. Cycle 20: After refmac, R = 0.2036 (Rfree = 0.000) for 6797 atoms. Found 11 (51 requested) and removed 25 (25 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.34 2.76 Search for helices and strands: 0 residues in 0 chains, 7155 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 7169 seeds are put forward Round 1: 547 peptides, 81 chains. Longest chain 15 peptides. Score 0.450 Round 2: 599 peptides, 76 chains. Longest chain 25 peptides. Score 0.526 Round 3: 585 peptides, 67 chains. Longest chain 32 peptides. Score 0.552 Round 4: 590 peptides, 75 chains. Longest chain 16 peptides. Score 0.522 Round 5: 603 peptides, 79 chains. Longest chain 18 peptides. Score 0.517 Taking the results from Round 3 Chains 72, Residues 518, Estimated correctness of the model 12.2 % 15 chains (151 residues) have been docked in sequence ------------------------------------------------------ 20082 reflections ( 98.41 % complete ) and 13547 restraints for refining 6938 atoms. 11008 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2389 (Rfree = 0.000) for 6938 atoms. Found 48 (52 requested) and removed 39 (26 requested) atoms. Cycle 22: After refmac, R = 0.2223 (Rfree = 0.000) for 6912 atoms. Found 26 (52 requested) and removed 32 (26 requested) atoms. Cycle 23: After refmac, R = 0.2119 (Rfree = 0.000) for 6895 atoms. Found 19 (52 requested) and removed 27 (26 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2069 (Rfree = 0.000) for 6874 atoms. Found 11 (52 requested) and removed 26 (26 requested) atoms. Cycle 25: After refmac, R = 0.2042 (Rfree = 0.000) for 6848 atoms. Found 12 (51 requested) and removed 25 (25 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.36 2.77 Search for helices and strands: 0 residues in 0 chains, 7194 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 7214 seeds are put forward Round 1: 553 peptides, 84 chains. Longest chain 17 peptides. Score 0.442 Round 2: 589 peptides, 74 chains. Longest chain 23 peptides. Score 0.525 Round 3: 592 peptides, 74 chains. Longest chain 22 peptides. Score 0.528 Round 4: 595 peptides, 74 chains. Longest chain 25 peptides. Score 0.531 Round 5: 545 peptides, 70 chains. Longest chain 19 peptides. Score 0.500 Taking the results from Round 4 Chains 80, Residues 521, Estimated correctness of the model 4.6 % 11 chains (98 residues) have been docked in sequence ------------------------------------------------------ 20082 reflections ( 98.41 % complete ) and 14243 restraints for refining 6938 atoms. 11906 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2425 (Rfree = 0.000) for 6938 atoms. Found 52 (52 requested) and removed 37 (26 requested) atoms. Cycle 27: After refmac, R = 0.2228 (Rfree = 0.000) for 6919 atoms. Found 24 (52 requested) and removed 34 (26 requested) atoms. Cycle 28: After refmac, R = 0.2158 (Rfree = 0.000) for 6883 atoms. Found 24 (52 requested) and removed 29 (26 requested) atoms. Cycle 29: After refmac, R = 0.2105 (Rfree = 0.000) for 6868 atoms. Found 13 (51 requested) and removed 25 (25 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2077 (Rfree = 0.000) for 6851 atoms. Found 10 (51 requested) and removed 25 (25 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.36 2.77 Search for helices and strands: 0 residues in 0 chains, 7205 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 7226 seeds are put forward Round 1: 518 peptides, 88 chains. Longest chain 16 peptides. Score 0.383 Round 2: 568 peptides, 84 chains. Longest chain 18 peptides. Score 0.458 Round 3: 567 peptides, 78 chains. Longest chain 24 peptides. Score 0.485 Round 4: 582 peptides, 81 chains. Longest chain 27 peptides. Score 0.487 Round 5: 571 peptides, 78 chains. Longest chain 21 peptides. Score 0.489 Taking the results from Round 5 Chains 81, Residues 493, Estimated correctness of the model 0.0 % 5 chains (48 residues) have been docked in sequence ------------------------------------------------------ 20082 reflections ( 98.41 % complete ) and 14893 restraints for refining 6938 atoms. 12830 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2424 (Rfree = 0.000) for 6938 atoms. Found 52 (52 requested) and removed 34 (26 requested) atoms. Cycle 32: After refmac, R = 0.2227 (Rfree = 0.000) for 6923 atoms. Found 31 (52 requested) and removed 29 (26 requested) atoms. Cycle 33: After refmac, R = 0.2156 (Rfree = 0.000) for 6905 atoms. Found 25 (52 requested) and removed 29 (26 requested) atoms. Cycle 34: After refmac, R = 0.2140 (Rfree = 0.000) for 6894 atoms. Found 18 (52 requested) and removed 28 (26 requested) atoms. Cycle 35: After refmac, R = 0.2095 (Rfree = 0.000) for 6878 atoms. Found 21 (51 requested) and removed 25 (25 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 2.77 Search for helices and strands: 0 residues in 0 chains, 7227 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 7239 seeds are put forward Round 1: 524 peptides, 95 chains. Longest chain 17 peptides. Score 0.354 Round 2: 555 peptides, 84 chains. Longest chain 16 peptides. Score 0.444 Round 3: 541 peptides, 78 chains. Longest chain 14 peptides. Score 0.458 Round 4: 553 peptides, 82 chains. Longest chain 16 peptides. Score 0.451 Round 5: 560 peptides, 79 chains. Longest chain 19 peptides. Score 0.473 Taking the results from Round 5 Chains 81, Residues 481, Estimated correctness of the model 0.0 % 10 chains (66 residues) have been docked in sequence ------------------------------------------------------ 20082 reflections ( 98.41 % complete ) and 14655 restraints for refining 6939 atoms. 12593 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2409 (Rfree = 0.000) for 6939 atoms. Found 37 (52 requested) and removed 32 (26 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2252 (Rfree = 0.000) for 6915 atoms. Found 26 (52 requested) and removed 28 (26 requested) atoms. Cycle 38: After refmac, R = 0.2200 (Rfree = 0.000) for 6903 atoms. Found 15 (52 requested) and removed 27 (26 requested) atoms. Cycle 39: After refmac, R = 0.2178 (Rfree = 0.000) for 6886 atoms. Found 16 (52 requested) and removed 26 (26 requested) atoms. Cycle 40: After refmac, R = 0.2154 (Rfree = 0.000) for 6870 atoms. Found 13 (51 requested) and removed 26 (25 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 2.75 Search for helices and strands: 0 residues in 0 chains, 7216 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 7240 seeds are put forward Round 1: 513 peptides, 92 chains. Longest chain 13 peptides. Score 0.357 Round 2: 571 peptides, 77 chains. Longest chain 24 peptides. Score 0.494 Round 3: 560 peptides, 78 chains. Longest chain 24 peptides. Score 0.478 Round 4: 570 peptides, 80 chains. Longest chain 19 peptides. Score 0.479 Round 5: 589 peptides, 84 chains. Longest chain 22 peptides. Score 0.480 Taking the results from Round 2 Chains 80, Residues 494, Estimated correctness of the model 0.0 % 15 chains (102 residues) have been docked in sequence ------------------------------------------------------ 20082 reflections ( 98.41 % complete ) and 14291 restraints for refining 6938 atoms. 12049 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2378 (Rfree = 0.000) for 6938 atoms. Found 52 (52 requested) and removed 40 (26 requested) atoms. Cycle 42: After refmac, R = 0.2221 (Rfree = 0.000) for 6921 atoms. Found 25 (52 requested) and removed 26 (26 requested) atoms. Cycle 43: After refmac, R = 0.2174 (Rfree = 0.000) for 6908 atoms. Found 20 (52 requested) and removed 31 (26 requested) atoms. Cycle 44: After refmac, R = 0.2150 (Rfree = 0.000) for 6884 atoms. Found 25 (52 requested) and removed 26 (26 requested) atoms. Cycle 45: After refmac, R = 0.2081 (Rfree = 0.000) for 6874 atoms. Found 21 (51 requested) and removed 25 (25 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.34 2.76 Search for helices and strands: 0 residues in 0 chains, 7190 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 7210 seeds are put forward Round 1: 486 peptides, 88 chains. Longest chain 13 peptides. Score 0.345 Round 2: 554 peptides, 85 chains. Longest chain 19 peptides. Score 0.438 Round 3: 578 peptides, 86 chains. Longest chain 17 peptides. Score 0.459 Round 4: 548 peptides, 78 chains. Longest chain 17 peptides. Score 0.465 Round 5: 544 peptides, 73 chains. Longest chain 30 peptides. Score 0.485 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 80, Residues 471, Estimated correctness of the model 0.0 % 10 chains (93 residues) have been docked in sequence Sequence coverage is 19 % Consider running further cycles of model building using 2hr2-3_warpNtrace.pdb as input Building loops using Loopy2018 80 chains (471 residues) following loop building 10 chains (93 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 20082 reflections ( 98.41 % complete ) and 14605 restraints for refining 6939 atoms. 12452 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2515 (Rfree = 0.000) for 6939 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Cycle 47: After refmac, R = 0.2366 (Rfree = 0.000) for 6895 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Cycle 48: After refmac, R = 0.2302 (Rfree = 0.000) for 6852 atoms. Found 0 (51 requested) and removed 10 (25 requested) atoms. Cycle 49: After refmac, R = 0.2284 (Rfree = 0.000) for 6838 atoms. Found 0 (51 requested) and removed 9 (25 requested) atoms. Writing output files ... TimeTaking 75.55